Over the last several years, ever since Nicholson et al. proposed dividing Anolis into eight genera, the topic of taxonomic splitting has periodically been discussed in these pages (for example, this post, its comments, and links to other posts).
The general question of when to split taxa recently has been revisited in several comments in AA. A week ago, David Hillis wrote:
“Anolis is a valid name for a monophyletic group on the Tree of Life. It is “special” as a genus only in that the genus name is used as part of a binomial for particular species. It doesn’t make sense to change the scope and application of generic names unless the names are actually misleading about phylogeny (e.g., if Anolis were polyphyletic, then that problem should be fixed). But splitting a valid, monophyletic genus into a bunch of smaller genera, and thereby needlessly changing the names of many species, without fixing any phylogenetic problems with the existing taxon names, is not science. It is just playing around with names. If someone wants to name the groups within genera, then do so…but there is no reason to change the meaning of a existing name (or the names of the all the affected species) in doing so. That is the kind of silliness that gives taxonomists such a deservedly bad reputation among biologists.”
Elswhere, David posted a flowchart on his recommended decision-making process about whether and how to divide recognized genera:
Ivan Prates, in line with comments he made in a recent paper on A. punctatus, then remarked:
“This seems more like a sociological matter.
During the ‘taxonomic revolution’ of the amphibians, about 10 years ago, the (perhaps?) most influential (or faster?) group was the splitter one, and their taxonomic scheme prevailed. Currently, nobody is upset about which species were once named as Bufo, Hyla or Rana. A few do care about Dendrobates – like Anolis, a sexy group with a body of dedicated investigators.
It seems that a single genus makes sense for the community that investigates dactyloid lizards more closely. On the other hand, those who deal with overwhelming levels of herpetological diversity in the tropics (waaaay beyond lizards) see benefit in more partitioned schemes, which correlate more closely to morphology and geography.
So, when we discuss names, it may be healthy not to forget about our diversity as investigators as well. About science, splitting Anolis is not science, but well, not splitting Anolis isn’t science either.”
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Thomas Sanger
“…more partitioned schemes, which correlate more closely to morphology and geography.”
In a discussion about a genus with rampant convergence the criterion of morphology seems like poor choice. Toepads and dewlaps are also perfectly acceptable morphological characters to diagnose Anolis as a monophyletic clade. Basing taxonomic decisions on geography feels subjective, a criterion that could be applied to different groups willy nilly depending on whether they are widely or narrowly dispersed.
John Sullivan
“Currently, nobody is upset about which species were once named as Bufo, Hyla or Rana.”
I know people who are still very upset about which species were once named as Bufo, Hyla or Rana. In fact, I thought I heard recently that the Bufo split was on the verge of being undone since so many people were upset about it. (I tried searching for some confirmation of this just now but was unsuccessful.)
Levi Gray
Agreed, many people are upset about Bufo and Rana sensu lato, and many are not using the names Ivan is referring to. When I teach herpetology, I explain the situation and make it clear that Bufo boreas and Rana pipiens are still “correct” binomials for those particular species.
Some of the Hyla (sensu lato) splits are still problematic for workers in the Nuclear Central American region (I can’t speak to lower Central American taxa but I suspect there are similar issues). Assigning individuals to certain genera based on morphology is incredibly difficult, as there are no traits that truly diagnose some of the groups. Sure, some subgroups can be ID’d easily (the large fringe-limbed treefrogs in Ecnomiohyla are an example) but in my experience even experts will consistently disagree on IDs. That has led our group to resort to sequencing some individuals just to try and place them in a genus. I just don’t think recognition of some Central American genera is warranted–though some clearly are due to monophyly issues.
The problem is compounded by practical issues with the recognition of so many hylid genera in Central America. Say you want to work on “Ptychohyla” and need to rely at least partially on museum collections, which is standard for many studies. You have to be very careful about what specimens to include, and you need to inspect every single specimen to be sure that it has been properly identified. Because these frogs are so difficult to ID, many will be in collections as “Ptychohyla sp”, which may not mean much considering the genus was found to be non-monophyletic and there are essentially no traits that can positively ID a frog to that particular genus. Also due to this problem, many actual “Ptychohyla” will be ID’d in collections as other genera and may be ignored unless the researcher is particularly thorough.
There is no easy fix. Some groups are just difficult, and Central American hylids are certainly one of those groups. Certain taxonomic changes may have been accepted by a multitude of authors but it does not mean the issue is settled, nor does it mean the changes have been a net positive for scientific ventures. I seriously wonder whether splitting up Hyla sensu lato has been a good thing.
Kevin de Queiroz
“… splitting Anolis is not science, but well, not splitting Anolis isn’t science either.”
That’s true under traditional nomenclature; however, if we were to move to a system of phylogenetically defined names (e.g., de Queiroz and Gauthier, 1990), then the application of scientific names would be dictated entirely by inferred phylogenies (science) and not by non-scientific judgements about which clades are to be ranked as genera.
Skip Lazell
I stand with David. The problem is that peer-reviewed publication helps get academic tenure = increase in $$, so round up your friends and agree to agree with all splits and get more money…. I have always called it Biostitution.
David Hillis
First, I agree with Kevin…it IS science if the taxonomy is clearly and unambiguously connected to phylogeny. That is why I am opposed to changing the meaning of a name that refers to a monophyletic group on the Tree of Life, just to make more names with different meanings. Then, the taxonomy becomes disconnected with the science, and it is all pretty arbitrary.
Second, the remark that “nobody is upset about which species were once named as Bufo, Hyla or Rana” is pretty funny! In fact, about 93% of the scientific papers on Rana pipiens (since the proposed name change to Lithobates) have continued to use the name Rana pipiens, and similar ratios apply to the other affected species of Rana. The vast majority of people have NOT recognized the proposed change to Lithobates, as they shouldn’t. The proposed change made no sense…the genus Rana (in the sense that includes Lithobates) is monophyletic in ALL analyses, whereas splitting the genera into smaller groups called Rana and Lithobates creates new phyloegenetic problems where none previously existed. For example, different data sets would put Rana sylvatica into Rana or Lithobates, and it isn’t clear that either of those poorly delimited groups is monophyletic even if that problem is solved. In addition,recognizing a genus Lithobates needlessly changes numerous well-used species names, including those of several model organisms. The proposal would also change the meaning of both names (Rana and Lithobates). The overwhelming majority of people who work on the systematics and biology of Rana (including me) continue to use Rana as the genus for all the New World species. Hyla is a different matter…some species, such as “Hyla crucifer”, made Hyla polyphyletic. Removal of those species from Hyla was the easiest way to fix a phylogenetic problem. Bufo continues to be the most controversial, with people arguing both sides. There are indeed monophyly issues with Bufo, and so the question is how to best fix those problems in the least disruptive way. I’d suggest that sinking a few small genera into Bufo is a lot better solution than splitting all the species out into multiple genera. But it isn’t clear yet how that one will fall out, as both sides have advocates. Of course, if we all followed phylogenetic definitions of taxon names, we would not have this problem.
Wolfgang Wüster
It is a pity that more people cannot be persuaded to use subgenera in situations like this.
The use of subgenera for Anolis would preserve the traditional genus-species name combination for ease of information retrieval while also adding a set of labels for the major clades within the group. More phylogenetic information, no loss of ease of information retrieval. Unfortunately, until major databases or organisations like SSAR start to take subgenera seriously, I don’t think they will find much traction.
Peter Uetz
Completely agree. Has anybody formally proposed subgenera for all anoles? I am happy to add those to the Reptile Database. BTW — you can search the database already for “Anolis Dactyloa” and similar combinations using the quick search on the home page (disclaimer: this may produce false positives occasionally).
Ivan Prates
Learning that many North American herpetologists got concerned about the changes proposed for Rana, Bufo and Hyla – while the Brazilian community, for instance, seems to have found it very instrumental – seems to reinforce my point that this discussion relates to how different audiences use taxonomic schemes.
Instead of explaining why the end of an Eleutherodactylus frog genus containing >1000 species made my field and lab work easier (not to mention comparisons in species descriptions), I would like to hear your thoughts about the following questions:
1. Other than based on convenience, how to objectively decide between two alternative taxonomic schemes when both reflect phylogeny (so presumably equally scientific), differing solely on which clades correspond to essentially arbitrary ranks (such as genus)?
2. How is it better to use Anolis and then adopt a parallel idiosyncratic taxonomy full of informal ranks (e.g., ‘species series’, ‘section’) and unranked designations (which sometimes correspond to invalid names, e.g., Phenacosaurus, Chamaeleolis) to be able to refer to sections of the dactyloid tree of life (which also makes anologists look completely crazy to other herpetologists)?
3. If field biologists based in the tropics feel that a given taxonomic scheme is more useful, should tropical biologists based elsewhere take their opinions into account?
Ivan Prates
Correction: a more accurate estimate of the number of Eleutherodactylus species would be >700.
David Hillis
“Other than based on convenience, how to objectively decide between two alternative taxonomic schemes when both reflect phylogeny (so presumably equally scientific), differing solely on which clades correspond to essentially arbitrary ranks (such as genus)?”
Response: If the names are phylogenetically defined, then the answer is objective. A name is clearly attached to a particular clade, and the oldest name for that clade has priority. Changing the meaning of a name to apply it to a different clade is the place where some recent taxonomy gets disconnected from phylogeny, and that is the problem that causes all the confusion and consternation.
“2. How is it better to use Anolis and then adopt a parallel idiosyncratic taxonomy full of informal ranks (e.g., ‘species series’, ‘section’) and unranked designations (which sometimes correspond to invalid names, e.g., Phenacosaurus, Chamaeleolis) to be able to refer to sections of the dactyloid tree of life (which also makes anologists look completely crazy to other herpetologists)?”
Response: Anolis is a widely-used name that applies to a monophyletic group on the tree of life. Disconnecting that meaning disconnects the name from a phylogenetic meaning, or at least confuses it. Using subgeneric names allows us to name new subgroups within Anolis, rather than to change the meaning of something that was already clear.
“Learning that many North American herpetologists got concerned about the changes proposed for Rana, Bufo and Hyla – while the Brazilian community, for instance, seems to have found it very instrumental – seems to reinforce my point that this discussion relates to how different audiences use taxonomic schemes.”
Response: There is one species of Rana in Brazil. In contrast, North Americans have to deal with the confusion of the paraphyletic proposed groups and name changes among about 50 species. Several of the affected North American species of Rana are widely used model organisms. So, I don’t think it is very surprising that North American biologists had a lot more to be concerned about in this case, and a lot more reason to object to the proposed change.
Thomas Sanger
“3. If field biologists based in the tropics feel that a given taxonomic scheme is more useful, should tropical biologists based elsewhere take their opinions into account?”
Ivan, are you suggesting that a biologist’s proximity to species should be taken into consideration when making decisions about nomenclature? I am not asking to be cheeky, but it seems like a criterion that cannot hold up to scrutiny. Anolis is spread across a very wide geographic area. What would prevent US biologists from insisting on a separate name for A. carolinensis or Cuban biologists from insisting that they have their own system? I could go on to many more spiraling examples (what about biologists that relocate?).
I think that opinions are being heard and discussed, but people are rarely focused on personal locations. Instead they are discussing nomenclature based strictly on the phylogenetic relationships of the organisms and what will be the least disruptive to the community as a whole.
Ivan Prates
Thomas, I’m definitely not – alternative taxonomies that depend on where you are is an absurd idea. Question 3 was meant to illustrate how motivations about splitting or not splitting Anolis are, in fact, sociological. The challenge is to come up with a unified taxonomy in the face of a heterogeneous body of investigators.
I’m surprised by how some of us seem to think so vehemently that choosing between two alternative taxonomic schemes when both reflect phylogeny is a scientific and straightforward procedure. Yet, the only insight about this matter (David’s) seems to be to stick to the oldest name. I’m not sure about how this criterion will help us not to get back to an all-inclusive, perfectly monophyletic Lacerta (snakes included).
I’m also surprised that so many people prefer to use an extremely idiosyncratic unofficial taxonomy in order to preserve Anolis sensu lato. The need of a taxonomy that correlates more closely to the group’s diversity is in our face, as indicated by the widespread use, resuscitation (e.g., Phenacosaurus, Chamaeleolis) and ongoing creation of new unranked names (e.g., Megaloa) by the community.
David Hillis
But what is the problem with using unranked names? Yes, we may need to name newly discovered clades…but why use old names that already have different meanings to do so? Anolis has a valid meaning, and it applies perfectly well to a particular monophyletic group of lizards. By tradition, we use that particular name as a genus, which means nothing except that it is the clade name that we use to form the binomial species names. Why mess that up, and mess up all those species names and their connection to the scientific literature in the process? We can still recognize other groups on the tree of life, above or below Anolis, with other names. And, we don’t really have to worry about what arbitrary “rank” they are…just how they are hierarchically related to one another. We do need to keep one name as a genus if we are going to retain binomial names under the current system, but I see no reason to change the meanings of generic names that apply to monophyletic groups on the tree of life. This is actually an easy problem to fix…we just have to use phylogenetic definitions of taxon names, rather than arbitrary applications and changes of the names on a whim. That way, the taxonomy can be connected to actual scientific principles, rather than making it the (nearly) meaningless mess that we are now in. I agree that the current practices are largely sociological rather than scientific, but I’m arguing against those non-scientific practices. Let’s bring the science back into taxonomy.
Ivan Prates
Well, it’s been the third day of discussion and I seem to be the only one who has been concerned about these matters. If there is absolute consensus within the community, this discussion seems unnecessary. Anolis it is.
Thanks David and all who dedicated their time to explain their viewpoints.
David Hillis
I think it was a good discussion, and I thank you for sharing your views as well, Ivan. I think many people profited from the open and civil discussion.
Scott Thomson
I will add a point or two here. First up David and Kevin both make good points on using phylogenetic criteria, and I agree with that. In saying that, no matter how much you want to use PhyloCode right now it is not accepted or understood world wide and less in some groups than others. I work with both living and fossil species, turtles. The turtle paleos almost exclusively use PhyloCode, but those working with living taxa will not use it. Why because 60% of turtle species are threatened or endangered and the IUCN, and CITES use the traditional ICZN code and until that changes they cannot use PhyloCodes because they cannot get legal protections in place. The point I am trying to make is there are driving forces in this beyond our control for the time being. I said recently to the turtle paleo’s when the world moves to PhyloCode I will too, without argument. Till then I just cannot, there is too much at stake.
I do not agree that the only reason to split a genus is a demonstration of paraphyly or polyphyly (though of course they are good reasons to lump or split) to me this leads to genera that are of no value, are undiagnosible, cannot be compared to the fossil record and basically make no sense except they are all related. The reverse argument of course on the frogs is, just sink them all into Anura, its monophyletic, thats objective, based on science. Why would you not do that? First because all the names are already in place, well that’s socialogical, Because there would be a net loss of information? that is subjective, but it is also one of the things the genus is meant to do, it is meant to convey information about a group of species that are related to each other.
I have no issue with subgenera, since I have sunk 3 genera to subgenera, am about do that to another and erected three subgenera in another genus but have only named 1 genus I think the numbers say I do not mind subgenera. The one genus I named was to solve a paraphyly by the way. But all this works both ways. If it is useful to and informative to split and it can be justified I have no issue with it. A part of taxonomy is to develop a useful working hypothesis that can be translated into usable information for other biologists, ie keys for field biologists among other things. There have been papers published on both ends of this spectrum in taxonomy and both over lumping and over splitting are damaging. Over lumping is seen as a cause of invisible extinction at the species level, with genera it changes the conservation value of the species, another cause for concern as it will underestimate the threats to a group of species. As taxonomists we need to think of the implications of the decisions we make. We are a base science on biodiversity. I see both over lumping and oversplitting as dangerous positions to take for species and are both a-priori decisions.
So on the topic at hand with the Anoles, I personally would not know if they should be split. But if the science has been presented and its good science on multiple datasets, then refute it or accept it. That’s another part of being a good taxonomist.
David Hillis
Phylogenetic definition of taxon names does not require PhyloCode. People can follow ICZN rules and still use clear phylogenetic definitions of names. The meaning of valid names for taxa should not be changed at someone’s whim. There is certainly no need to change validly named monophyletic groups, like Anolis. If someone wants to name other unnamed groups on the Tree of Life, then go ahead and do so. But there is no reason to change the meaning of a validly named, monophyletic clade. Otherwise, it does indeed turn taxonomy into a sociological preference, rather than a science. Taxonomy does not inform biology if names change in meaning at someone’s whim. Taxonomists who consider themselves scientists should resist that kind of behavior.
Scott Thomson
Yes but remember though that the definition and diagnosis of a genus is based on one species, the type species. By original or subsequent designation. All other members of the taxon should agree with the diagnosis of the original type species. If they do not then you have a polytypic genus that may be monophyletic but is now loosing its definition anyway to cope with the new species being added that are forcing the relaxation of the original definition to fewer and fewer characters.
Also consider that limiting yourself a-priori to a single reason for splitting, or lumping, your not really recovering the tree of life, your recovering the tree of the history of nomenclature.
I do not promote lumping or splitting, I sit middle ground on this. But examining the concept of the genus forces you to look at both sides of it. Cheers.
Scott Thomson
“All other members of the taxon should agree with the diagnosis of the original type species. ”
Sorry I meant to say there that all other members should agree with the original diagnosis of the genus as represented by the type species. Not the diagnosis of the species itself.
From my limited knowledge of Anoles I would suspect they are candidates for subgenera though, based on possession of distinct characters by all members such as dewlaps. I could be wrong on that though.
Cheers
Wolfgang Wüster
I don’t see how we can tie our concept of a genus to the original diagnosis. Surely the REAL diagnosis of a genus (in terms of the overall envelope of variation) changes with the addition of any species beyond the type species or the original set of species in any case. Adhering to the original diagnosis would force splitting every time a new, apomorphic species is found to be clearly nested within the original genus by a phylogenetic analysis. The *operational* diagnosis of a genus therefore inevitably changes all the time with the discovery or inclusion of additional species and/or new discoveries on the anatomy of members of the genus.
David Hillis
Even Linnaeus was quite clear on the point that a genus gives us a diagnosis, and NOT the other way around:
“Characterem non constituero Genus, sed Genus Characterem”
-Carolus Linnaeus (1751, in Philosophica Botanica).
Darwin also commented on this point, and noted that phylogeny was the central idea of taxonomy (although the word “phylogeny” had not yet been coined):
“Such expressions as that famous one of Linnaeus…that the characters do not make the genus, but that the genus gives the characters, seem to imply that something more is included in our classifications, than mere resemblance. I believe that something more is included; and that propinquity of descent—the only known cause of the similarity of organic beings—is the bond, hidden as it is by various degrees of modification, which is partially revealed to us by our classifications.”
-Charles Darwin (1859, in The Origin of Species)
In other words, phylogeny is what defines genera (and other taxa), and from them, we can get a diagnosis. That diagnosis will obviously change through time as we discover more species within the genus. ICZN rules require a diagnosis in the description of a taxon, but it doesn’t even need to be correct, and certainly we don’t rely on the original diagnosis to determine the limits of a taxon. If we did, it would be pretty hilarious, as most early taxa were “diagnosed” by simple characters that would prove completely useless today.
We do have to make sure that the type species of a genus is included in the genus, of course. But that is not an issue if we leave clade names alone, except to correct phylogenetic problems. That is merely part of the “valid name” question.
If we don’t retain the original meanings of clade names, and allow people to split them whenever they feel like it, when will it end? Today, someone may want to split Anolis into seven genera. Tomorrow, they will want to split each of those seven into ten more. If such arbitrary changes in the meanings of names are allowed, then the only logical stopping place is when every species has its own genus, at which point genera will become completely pointless. We are almost at that point with Dendrobates and some groups of turtles now.
Darwin was right: our classifications have one purpose—to reflect “propinquity of descent”. Valid names that do that (i.e., apply to monophyletic groups on the Tree of Life) should be left alone. Changing them for social reasons is not merely annoying, it is scientifically unsound and unjustified, and detracts from the prime connection between phylogeny and classifications.
Scott Thomson
I have not once disagreed with you on the decent process identified by Darwin I started out stating that phylogeny is the objective method part of this issue. I agreed with both you David and Kevin on this. Whether Linnaeus knew what he was on about is another matter. But lets leave that debate.
Where we disagree is on when and why you can change things, besides paraphyly, in some groups these very large genera that are undiagnosible only exist because of historical reasons. There is no science supporting these large genera except that despite the number of taxa and the structuring within it the whole lot is monophyletic. I do agree with you that its not a process to be taken lightly and any taxonomic change to a group should be undertaken with multiple datasets and with lots of justification. That is to avoid your scenario of it carrying on ad nauseum.
To use a turtle example since I know them better. The genus Emydura was proposed to be synonymous with Elseya by Gaffney 1979, supported by McDowell 1983. This was not done to solve a paraphyly it was done because they could not distinguish the genera. Georges and Adams 1992 showed the genus Elseya to be paraphyletic with respect to Emydura but rejected the notion of synonymy but rather chose to split, leading to my naming of Myuchelys. During this time within this super clade Emydura have been named Rheodytes, Elusor, Flaviemys and Birlimarr. Only one of these genera is monotypic (Elusor) if we include the fossils. Among the fossils that can be positively identified to one of these genera we have Elseya and Myuchelys at 103M yrs, Flaviemys, Rheodytes and Birlimar all around 45-50M yrs, Emydura about 3M yrs, only Elusor has no fossil material to date. If we had recognised this genus Emydura for all of this so much information on the relationships, zoogeography, paleozoogeography and even things such as habitats and ecology would have been lost and hidden in a system very few outside pure taxonomy understand or even care about.
The genus is a combination of two things objective phylogeny and subjective information, yes I have published that (Georges and Thomson, 2010), it cannot be of any use if it is one without the other. The clades are their whether you name them or not, the genus is about naming certain clades, and not others to portray useful information about relationships. Information that is useful to all branches of science, not just systematists. Refusing to permit any change to this except under objective refutation of the hypothesis is under utilising the purpose of the genus and leads to an inbalance as to which genera are well resolved and portray good information and those that are no more than a bucket. What your supporting with only paraphyly being an option for changing the taxonomy, leads to bucket genera of no use to anyone. We have to find a balance between between what your saying and reasonable grounds for splitting, or lumping, of genera. I totally agree, however, going to far the other direction is also undesirable.
David Hillis
“bucket genera of no use to anyone”
This appears to be the fundamental disagreement. I see all well-supported clades on the Tree of Life as important, and knowledge of those clades is very useful to many biologists. If they are important to biology (like Anolis), then we should name them. Once we name them and show that those names refer to a monophyletic group, we should not change the way we use the name, UNLESS we discover that we were wrong about the phylogenetic relationships and the named group is not actually monophyletic. In that case, we should fix the problem with the least disruption possible. If we have have need to refer to smaller clades within Anolis, then name those clades as well…but don’t change the meaning of the name Anolis in doing so. That way, classifications are meaningful and consistent with reference to phylogeny. In that way, we can keep taxonomy a part of science, and not just something that is subject to social whims.
Scott Thomson
Oh in response to Wolfgang, I was a little unclear. The original diagnosis is your benchmark and of course it will evolve. Which means it is no longer the original concept anyway. Hence I see no argument for preserving it if a good reason not to arises. My point on the type species is that as more species are added the definition of the genus may be overridden by the internal structuring of the phylogeny in the genus. This structuring may get to a point where it it is useful to recognise it. That could be done with subgenera, as I said I get the feeling that Anolis could have gone this way as you also pointed out Wolfgang. However, hypothetical case, it could also come to the point where there is such deep structuring that more sense of the relationships can be done with new genera.
Cheers
Wolfgang Wüster
Picking up on the “usefulness of bucket genera” issue: I think systematists and phylogeneticists tend to overestimate the number of people who are overly bothered about the finer phylogenetic structure of these groups and want to see it reflected in the genus-level nomenclature. I very strongly suspect that a very considerable majority of the scientific name user community simply want one thing: a single binomial that they can type into Web of Knowledge, the Zoological Record, Genbank or whatever, and obtain all the information they need on the species they are interested in. Change for the sake of change disrupts that ability, and tends to go down badly (thereby further harming the reputation of taxonomy).
Moreover, the minority who are genuinely interested in the biogeographical history of a group, or the evolution of traits therein, or other similar evolutionary questions, will be best equipped to avail themselves of the phylogenetic information they need for that purpose, irrespective of whether the group is a large bucket genus or not. It is the community of users further removed from the practice of taxonomy that will be much less equipped to make the connections between older and newer names, increasing the likelihood of confusion. The literature on snake venoms is a fine example of that.
Clearly we don’t want to freeze nomenclature, and actively misleading nomenclature (i.e., recognition of non-monophyletic groups) must be remedied, but beyond that, I think David’s flow chart is entirely apt and appropriate.
Jonathan Losos
Couldn’t agree more. Well said, Wolfgang! Name changes are very disruptive to users far removed from systematics and, in any case, if you’re interested in the phylogenetic relationships of group members, then look at the phylogeny!
David Hillis
I have spent my career developing applications of systematics, and working to get biologists in other fields to take the field of systematics seriously. The field has made enormous progress in my lifetime, and phylogeny is now viewed as a central principle throughout biology. Pick up almost any biological journal, and you will see phylogenetic trees and their applications. That is a great success of systematics.
Unfortunately, many people still equate the field of systematics with the much narrower field of taxonomy, or the even much narrower practice of nomenclature. Biological nomenclature has become so disconnected with science in recent years that egomaniac hosers now run rampant, proposing changes in the meaning of names for valid taxa at their personal whim. There are now almost too few professionally trained systematists to stop this silliness, or who are willing to speak out against this unprofessional practice. The field of biological nomenclature has become so pitifully neglected that many professional systematists have simply ceased caring about or paying any attention to biological nomenclature. I can easily understand why.
There are only three systematic biologists elected to the entire US National Academy of Sciences. Why so few? Because the field of systematics isn’t taken seriously by many scientists, due to its unfortunate association with biological nomenclature. Those of us in the field of systematics complain about the lack of funding for systematic biology, and yet we allow our discipline to be dominated by petty people who only care about attaching their personal names as authors of new taxon names, thereby “making their mark” by disrupting the current taxonomy as much as possible. If biological nomenclature is going to survive as anything except an arcane art form, that has to stop.
Taxonomy (the study of biological taxa) is an important scientific discipline. Like most fields of science, the field of taxonomy has benefited enormously from our recent advances in phylogenetics. Nomenclature (how we name taxa) is merely a service to the rest of biology: it should inform, to the best of our ability, other biologists about our understanding of biological taxa. If we discover and provide evidence for taxa, and then name them, those names should not change unless we discover that we were wrong about the taxa. No other field of science constantly changes the meanings of its terms based on personal whims. Changing the meanings of names disconnects the names from any clear meaning and makes a mess of the scientific literature. That is not a service to science; that is a disservice.
David Wake
I know I am a few days late getting into this thread, but I have read it with great interest and hate to see it drop or get lost. David Hillis — you need to publish your thoughts on this somewhere where more people will see them!
With respect to what started this thread, I will admit that it is not easy to know what would best serve the general interest at this point. I suspect that most of us use as a starting point not Linnaeus but something close to what we first learned. Thus, no-one thinks that we need only Lacerta or Rana or Salamandra, but more genera in each clade, so that utility is served at some level. I could live quite happily with a classification that uses fewer genera and more subgenera, because I think that would serve many interests. It would enable us to provide some level of phylogenetic information beyond what would be gained from every species in its own genus, at one extreme, and all species in one genus, at the other. But I am wishy-washy as to where this begins or ends. As a curator of a major collection, I would love to see Anolis used sensu lato, with subgenera, and as a general evolutionary biologist that also is what I would like to see. I think subgenera is the easiest and, at least as long as the present Zoological Code is in place and until we have a Phylocode, most communicative way of providing phylogenetic information, incomplete though it is. I specialize in salamanders, where subgenera are becoming more and more acceptable. Thus, I find it more informative to include the European and American species of Hydromantes (sensu lato) in a single genus, which is clearly monophyletic, with many unique synapomorphies and no close relatives (even unclear which is its closest relative), than to have the European species separated off into one or two different genera whose name gives no clue that they have close American relatives – a continuing biogeographic enigma that stimulates thought if no much action, as yet. Also useful is the separation of eastern and western clades of the large monophyletic Plethodon (with 55 species) into two subgenera, and the even larger (130 species) Bolitoglossa of tropical America into 7 subgenera. However, it seemed more useful when breaking up the polyphyletic tropical American group Pseudoeurycea to use genera rather than subgenera because of continuing issues in getting a robust phylogenetic hypothesis for the assemblage. Lost in the shuffle is the “regrettable” (because the genus gave the characters, paraphrasing Linneaus) sinking of the morphologically and ecologically very distinct Lineatriton into the remnant Pseudoeurycea — for the evolutionarily fascinating reason that, while monophyletic, it was a very close relative of the Pseudoeurycea generotype P. leprosa. My point in all of this is that practitioners in different areas should try to reach some agreement as to what taxonomy best serves the community of direct users and enables them to most readily communicate to the broader community of biologists and the public.
David Hillis
I think we are in full agreement, David Wake. I’d also retain the meanings of the monophyletic genera Hydromantes and Bolitoglossa, and i think it is reasonable to modify the polyphyletic genus Pseudoeurycea to create monophyletic genera. I think all of that follows exactly the irreverent (and somewhat tongue-in-cheek) flow cart I created as a meme (the chart that headed this post). I’m glad that you are embracing the concept of subgenera, which can be used to identify many more important clades. I think subgeneric names need to be used much more often, and that they would take a lot of pressure off the “need” to subdivide existing genera.
Scott Thomson
Please do not get me wrong I largely agree with what both you and Wolfgang have said. I have no plans of splitting up some group somewhere I am generally rather conservative as a taxonomist. I am largely trying to debate issues that I think need to be debated more.
I agree with Wolfgang that a vast majority of people just want a search term. A label. They do not care any more than that about it. I think that is a little unfortunate, but I cannot blame them for that either.
One of my difficulties is that I am frequently asked by molecular systematists to identify all these fossil turtles and tell them where they fit with respect to modern taxa so they can use it for dating the tree. How exactly am I supposed to do that when the modern taxa are not diagnosible. Then they try do it themselves, which would be best described as they guess, and we get, real example, 3 papers in 2 years using the same data, the same genes, from the same specimens with 3 completely different sets of dates on the tree. All of which give the entire evolution of the Chelodininae at between half and 1/4 the age of the oldest fossil that I can place in that same tree. So yes I am looking for better ways. One thing I would like is that if you are going to describe something do some real morphology, and I do not mean colors and scale counts, I mean morphology that may be preserved in the fossil record. Osteology.
On nomenclature that you brought up. I personally happen to like nomenclature, probably because of the history of it. I am not suggesting it is more than you say it is. Just a field I happen to enjoy. Nomenclature has taken some big hits in recent years and the reasons you elaborated on are some of them. My views on Hoser and his methods are published, I am one of those attempting to put the brakes on his behavior. I do not care if he describes the odd species, as long as its original work, with a scientific underpinning in a valid journal. But what he currently does is pure self indulgent rubbish. He is not the first to do this but he has probably been the most controversial. I think though that Biological Nomenclature became disconnected because of people like Hoser, particularly if you take it back, Hoser at 730 taxa, Wells and Wellington (1980’s) 600 taxa, Hawksworth not sure how many taxa for him, Pic (1950’s) 30000 taxa. This has been sliding for a while. Remember also that while you clearly distance yourself from Nomenclature in what you said above, reality among general public and many biologists is that systematics, taxonomy and nomenclature are all the same thing. Of course they are not. In thanking the 70 authors who participated in my recent paper, Wolfgang here among them, I said that the the fields of taxonomy and nomenclature were in need of help because what was being done to nomenclature was having flow on impacts to taxonomy, and as you seem to indicate, to systematics. The damage is being done.
It has been an interesting discussion, thanks for that.
Paul Kelly
To a purist the reason to split a genus is to better express phylogeny. In the early battles among taxonomists as to how to turn a tree into a classification, some actually proposed that any taxon with more than two subgroups was deficient as it would not fully express the data. Under this unworkable philosophy any genus containing three species would have to be divided, either into two genera or into two subgenera to group the two most closely related species. I saw some insect classifications done that included more than fifty levels, with a pile of super-, sub-, meta-, and infra- categories. This produced unworkable, though information-rich schemes. Some taxonomists seem to ignore the fact that to many biologists taxon names are needed so that one can make meaningful generalizations about groups, even those that (gasp!) may be paraphyletic. In North America several snake genera are likely polyphyletic as presently recognized. but group species with a host of morphological and ecological similarities.
Bob Powell
I am not a systematist so my opinion might add little to this discussion. However, labels matter for many reasons (as has been acknowledged above, albeit somewhat disparagingly). Yes, systematics should drive taxonomy and taxonomy should provide an informative and useful nomenclature. The latter should not change arbitrarily at the whim of someone seeking to make a name for him- or herself. At the same time, systematists have a responsibility for translating a phylogeny into an appropriate nomenclature. A failure to do so serves no one. So, if subgenera provide the necessary information while maintaining nomenclatural stability, let’s use them — but let’s also acknowledge that by omission from the binomen they provide fewer insights than splitting a genus and creating new names that clearly identify the clades.
That said, I see a philosophical disconnect in recent taxonomy. Although “splitters” endeavor to break up some genera (in fact, this entire thread to some degree reflects a reaction to such an attempt), I think the recent tendency in herpetology is to “lump” species into large genera and promote the use of subgenera to reflect distinct clades (some biologists who focus on frogs might be exceptions). In sharp contrast, herpetological systematists in recent years have largely abandoned the recognition of subspecific clades, in effect declaring the species the terminal clade in any phylogeny. I suggest that much of the reason for avoiding subspecies is that the term has been so variously used as to be almost useless (some have declared that subspecies be used only for “incipient” species, another term with variable definitions, whereas others have used subspecies as a convenient means of recognizing infraspecific variation at various levels).
So, are we being inconsistent in our aversion to splitting genera while avidly splitting species? I suspect the former will continue to plague those of us who rely on an informative nomenclature while ardent proponents of either view make valid points in defense of their preferred philosophy. I also suspect that the latter will continue to the extent that subspecies (and the accompanying trinomial) will disappear entirely. I don’t necessarily see either of these as bad things — and they will certainly continue to provide fodder for discussions among reasonable biologists just as they will serve as ammunition for less-than-amiable arguments among others.
One final point regarding the utility of nomenclature is that, while a reliance on morphological characters has obviously led to recognizing some errant taxa, the dependence on genetic data has led to many taxa that cannot be diagnosed without sequencing DNA. So, I leave you with this question: Do names of clades truly service the biological community if the labels cannot with certainty be assigned to groups of or even individual animals?
David Hillis
Bob Powell:
It is a bit off-topic for this thread, but since you asked about species and subspecies, here is my opinion on that topic:
First, I don’t think either species or subspecies are “clades”. Species are lineages (the branches on the tree of life). Sexual recombination among individuals results in tokogenetic relationships within species. Clades, on the other hand, are monophyletic groups of lineages on the tree of life. Rather than being defined by tokogenetic relationships, they are defined by phylogenetic relationships.
Traditionally, subspecies are geographical races of species. In other words, they are geographically distinct populations that nonetheless meet and interbreed at contact zones. Sometimes, these contact zones are very broad, as with broad-banded versus southern copperheads. If the contact zones are very narrow, and there is strong evidence that the contact zone is a genetic sink (there is no gene flow across the zone, because of strong selection against hybrids), then I agree that the two entities can be considered separate lineages, and hence species. But in many recent cases, as with the copperhead example, there is abundant evidence that the contact zone is NOT a sink, and that there is NO selection against hybrids. In this case, I disagree strongly with the authors who proposed to split these subspecies into distinct species. That is inconsistent with any lineage species concept…there is a huge area where these two forms intergrade, with no evidence of any loss of fitness. Thus, the two forms are geographical, intergrading races, or subspecies.
I think we will soon see a backlash against the splitting off of geographic races as species as well. Frank Burbrink (who was an author on the copperhead example I mentioned above) and I plan to write a pro/con article about this together, each arguing our respective points of view. Hopefully, this will re-kindle the conversation about subspecies.
Subspecies are unpopular right now because they were long abused in several ways. Inappropriate uses include (1) to describe non-geographic “varieties”; (2) to arbitrarily break up clines; and (3) to describe distinct, isolated lineages that clearly are species. But used in proper context to designate a geographically distinct race, they are certainly reasonable and often useful. They are rarely used in some groups, for several reasons: Groups like freshwater fishes have discrete ranges, so taxa don’t interbreed over broad areas. And many groups are too poorly studied to understand geographic variation. But in well-studied terrestrial groups (like herps), subspecies are perfectly reasonable and useful taxa to designate intergrading geographic races.
Bob Powell
I’m not sure I understand your distinction between lineages (that include species) and groups of lineages (your definition of a clade if monophyletic). If species did not exist through time, they’d be defined solely by tokogenetic relationships, but because to do exist over time, they exhibit phylogenetic characteristics (namely ancestor-descendant relationships). So, why aren’t species clades? This is especially true if subspecies are recognized. Each geographic entity presumably represents a lineage, which would render the species a “group” of lineages defined by phylogeny.
Again, remember that I’m not a systematist, so what I’m arguing is that many of the disagreements over splitting or lumping (that affect all of us, systematists or not) ultimately depend on one’s definition of a genus or species or even subspecies. If we could all agree on the same definitions and apply them consistently, the arguments would disappear and everyone could concentrate on generating the evidence that would allow classification to best reflect the considerable complexity inherent in nature.
David Hillis
A lineage is a group of interbreeding individuals, extended through time. The relationships within the lineage are tokogenetic…so two parents recombine their genes to produce their offspring. Those parent-offspring recombination events extend through time in a series of ancestral-descendant populations, but those relationships are not phylogenetic….there is always a single reproductively connected group, which becomes a lineage as we extend it through time. This reproductive group (the lineage) does not split into two…or rather, if it does split, that is a speciation event, and there are now two lineages (species). The tokogenetic events define the boundaries of the lineage. The lineage begins when it splits from another lineage…that is a phylogenetic split. In that case, one lineage splits into two…unlike tokogeny.
Imagine an actual tree. The lineages are the individual branch segments on the tree. There are also groups of branches that share a common ancestral branch segment…those are the clades. A clade consists of an ancestral lineage and all of its descendant lineages. The individual lineages (branch segments on the tree) are the species.
Subspecies differ from species in that the subgroups are not fully separated as distinct lineages. There may be selection for different traits in different parts of the range that leads to divergence, but the groups are still reproductively connected. Or, perhaps the lineage started to separate into two lineages in the past, but then the lineages came back together and merged again. Either way, we can see at present that the two groups are not reproductively isolated from one another, and so they are not distinct lineages. They are geographically differentiated parts of the same lineage. In the case of the copperheads, the western ones differ in many ways from the eastern ones (size, color pattern, diet, behavior, etc.). But the two forms are connected by a continuous series of intermediate populations. That shows that there is indeed gene flow between the two, and no evidence of any selection against hybrids. Thus, the boundaries of the lineage (the species) include both forms (broad-banded and southern copperheads). We could just ignore the geographic variation, and that is what we do if we just talk about the species and ignore the subspecies. But, if we are interested in the real biological differences between copperheads in the eastern and western parts of the range, then it helps to have a way to refer to these different groups. Designating them as subspecies allows us to do that.
Note that I don’t care if people use subspecies, or choose not to. But, I do care that some people are artificially splitting up single lineages into multiple species, even when we have clear evidence that the designated groups broadly intergrade. In that case, there is positive evidence that the groups are NOT distinct species.
Scott Thomson
“At the same time, systematists have a responsibility for translating a phylogeny into an appropriate nomenclature. A failure to do so serves no one.”
Yes agree with you on this, I do not think changes should be made lightly I agree with I think everyone here on that. My main argument has been about what constitutes a good reason.
On the issue of subspecies, I suspect that what you say is largely correct. I have long ago avoided using them to any great degree. The only ones I have formally recognised was the subspecies of Emydura macquarii, I accept the ones in Chelodina mccordi in my reviews though I had nothing to do with their recognition. The interesting thing in the later case is that one of the taxa in there was named as a new subspecies and declared as a subspecies so that it would automatically receive CITES I status to protect it. That argument troubles me as I find it circular. There are a lot of subspecies still being used in turtles though the erection of new ones is declining.
On subgenera I totally agree they are a very good and underused means of demonstrating structuring within a genus. They should be used more often than they are. I think there are inconsistencies here. As you have pointed out. Basically I do not think setting what is effectively a rule over how to handle genera is good science. I mean David’s points are very good and valid as is his meme, but absolute rules prevent advancement.
As to your final point. Well I am a taxonomist and paleontologist. So I am not going to get DNA out of many of the specimens I examine. They must be compared to living taxa using osteology. In saying that I do not think we should rely on morphology or molecular data alone, but both should be in there. I would also add that good statistical analysis of morphometrics is also needed as a minimum for suggesting changes to the phylogeny. Publish the trees if you wish, no problem with that. But test the databases against each other, use total evidence or scaffolding, get a good consensus tree then start making your changes. This will avoid molecular species, which are also of no use to anyone. I mean speaking as a paleontologist throw all the DNA sequence data in my face you like, you have no data I can use, and if there are known fossils in the group then you have not examined all the species. However this is a little off topic, apologies for that.
Cheers, Scott
Nico Franz
Spirited discussion. Somehow I feel this is related.
http://biorxiv.org/content/early/2015/07/10/022145
If we design platforms that are highly effective at resolving evolving taxonomic name:meaning relationships, then the science can proceed effectively (whether there is stability in inference, or not so much).