Category: New Research Page 46 of 67

It is very clear that most people who have posted to the blog site are quite uncomfortable with any proposed change to the concept of one big happy Anolis. What shines through to me in the posts is how deeply emotional the thought of this change is for many of us. I think I understand this emotion and hope to try to persuade you to let go of it by presenting this short story. I did my dissertation on Norops humilis in Costa Rica. The emotional side of me likes to think that, when this scientific name is mentioned in the future, my name and my work will forever be associated with it. Because of that, when Gunther Köhler and Kirsten Nicholson (my very own former student!!!!) wrote a paper demonstrating that I had not performed a dissertation on N. humilis but instead had worked with N. quaggulus, I took the news quite badly. In fact, to this day I struggle with this news because I find it difficult to deal with an emotion that says my work will be lost to the scientific community because of this name change. Obviously, this is totally illogical. The scientific community has been quite resilient to such changes. Classic works on North American Natrix were not lost to careful scientists by a name change to Nerodia. Blair’s work on North American Bufo will continue to be found and cited by anyone working with evolution of Anaxyrus. In the case of my N. humilis work, the thing that has gotten me over the emotional hump is the exciting biology that becomes clear if N. humilis and N. quaggulus are distinct species. Jenn Deitloff, Kirsten Nicholson, and I have been looking for the contact zone between the species I studied at La Selva and the species in Costa Rica that I thought I was studying. We want to determine how two species can maintain separate evolutionary trajectories given that there is no obvious boundary to their dispersal and their dewlaps, at least to my eye, are virtually identical. Köhler’s work seems to indicate that anole biologists have vastly undercounted the real species richness within Norops (and probably the other genera) because some characters, like dewlap color, may operate on a much more subtle level than we have allowed ourselves to consider. If I could have forced the world to succumb to my emotions, I would have, and these anoles would still be one big happy species rather than the several smaller lineages that character data seem to indicate they are. I could cling to N. humilis by pointing to a node on the tree and argue that, because of taxonomic stability, this should continue to be that species so that my La Selva work would maintain its association with that taxon. But, I would miss out on the interesting biology that emerges from simply letting go of that concept.

I see similar advantages to breaking anoles into eight genera. My experiences have caused me to develop a completely different search image for anoles in the genus Dactyloa than I have for those in the genus Norops. In helping to generate the revised taxonomy, I think I learned something interesting about anole ecology, and that is that it may be shaped by an origin of the group in the crowns of canopy rainforest trees in South America followed by a series of biogeographic events that brought them down to the leaf litter. I don’t recall our notions of evolution of anole communities being framed in quite this way. The fossil record and the topology of the phylogenetic tree led us to that insight. Discussions among the authors of the revised classification, during which we forced ourselves to use eight generic names instead of one, helped us gain those insights. We encourage the use of our taxonomy because it helped us see things that we might not have seen and we are confident that this may happen to others. As foundational as Schoener’s studies of one- and two-species islands were (and are – this work certainly shaped my interests), we think it would have been improved had he been forced to recognize those anoles as belonging to the genera Dactyloa and Ctenonotus. We suspect he would have analyzed the sets of islands separately and might have generated discussion among ecologists about degrees of freedom in comparative studies a decade before that discussion actually emerged. We think the taxon-loop vs. character-displacement argument would have been refined had the Dactyloa islands been viewed separately from the Ctenonotus islands. The Dactyloa-islands likely would have been described as fitting most strongly with the taxon loop hypothesis (large ancestors forced to become small with the first small species being doomed to extinction by the next smallest species – or large colonists reaching these islands, leading to the same process) and the Ctenonotus islands likely would have been described as most strongly fitting the character displacement hypothesis (mid-sized ancestors with a niche focused toward the ground diverging to make room for the next mid-sized colonists). We think Losos’ analysis of evolution of ecomorphology of Puerto Rican anoles would have been improved had he been forced to use the genera Deiroptyx and Ctenonotus.

I think the real intent of this blog is expressed in Glor’s posts. In my opinion, he is clearly asking the community of anole systematists to band together as a unified voice against acceptance of the proposed new taxonomy. Obviously, the community of anole systematists has never been of one mind on this topic and I would hope that the community would recoil at the thought that we ever should be. The notion that the world recently came to accept a single large genus Anolis as the only viable concept can be rejected by the observation that some in the community of anole systematists continue to publish under names such as Dactyloa, Norops, and Ctenonotus (e.g. Savage’s book). Given what is happening with so many other large, cumbersome genera, I think it is inevitable that a revised classification of anoles will happen and those who are fighting so hard to prevent it will find their careers intact when they cross that inevitable threshold. Once there, I think they will wonder why they fought so hard against change.

KIRSTEN E. NICHOLSON, BRIAN I. CROTHER, CRAIG GUYER & JAY M. SAVAGE (2012). It is time for a new classification of anoles (Squamata: Dactyloidae) Zootaxa, 3477, 1-108

To some degree, I am playing Devil’s advocate in supporting the split of Anolis – but I do think there are valid arguments that need to be considered.

There are a number of assumptions that, if proven to be false, weaken my argument:

1. As a clade, anoles are older than the KT boundary – 65 million years. The estimates from Nicholson et al. are much older than that, but if you were to choose a date where splitting up vertebrate genera might make sense, 65 million years is not unreasonable. It is likely that coalescent methods will make the estimated age of anoles younger than the 95 million years in the paper, but I’m going to guess older than 65 million years. You may feel that clade ages are irrelevant, but I’m willing to bet that most people would have some age that they would say is too old for any genus (500 million years?)
2. The Alfoldi et al. (2011) tree is pretty accurate and the following aspects of that tree will remain after adding taxa and more data. Starting with the Norops clade or genus (see below for a discussion of why Norops), there are 8 very well supported clades (black dots on the Supplemental figure). There are very short branches between 4 of those groups, representing a rapid radiation such that only 3 of 7 possible inter-group relationships are well supported. Anolis lucius and  A. argenteolis were left in Anolis by Nicholson et al. because A. argenteolis represents the biggest conflict between mtDNA and nuclear DNA and is placed with high confidence with the Anolis clade in Alfodi et al. – I assume that the nuclear tree represents the correct placement of that species.
3. If Anolis is split up, the usage of the word “anole” would increase and refer to all 8 genera to a degree that would minimize workers not knowing that these 8 genera are monophyletic.

One narrative that needs to be considered (see Rich Glor’s excellent post on the history) is that the impetus to split Anolis comes from those who have primarily worked in Central and South America, where the two most disparate (by time) clades of anoles co-exist. If there are non-systematists working on anoles on the mainland it would be useful if they recognized the deep split between two clades of species now in the same genus, especially if clade names fail to be used outside of those whose focus is phylogentic trees. The problem has been that if Dactyloa and Norops are used on the mainland, then a bunch of other generic names are needed for the Caribbean species that fall between the two genera on the tree, with 8 being the minimum number of very well supported groups (again with an assumption that the nuclear DNA framework is robust).  To split Norops further might lose the great story of the reinvasion of the mainland from the Caribbean (Nicholson et al., 2005). From the perspective of those working on the mainland, 8 is a logical minimum number. Given the lack of resolution between the 8 groups, 8 clades is more information than 1 and not much is lost going to 8.

It is important to ask what workers on mainland anoles other than Nicholson et al. think about splitting Anolis. What does Laurie Vitt think, for example?

Another aspect of genera that hasn’t been touched on yet is morphological dissimilarity. Although there is no agreed upon (or necessary) level of dissimilarity needed to recognize a genus, my personal feeling is that if two species are in separate genera, it should not be difficult to tell them apart as species.  I think that this is one reason that I am opposed to the excessive splitting of Bufo and Rana that have been proposed. (To really make this a really good argument, I would need to find some specific cases where the new Frost et al. 2006 genera are difficult to tell apart as species – I’m just assuming that this is true –). In any case, Anolis is not like Bufo – the species are distinct and there is plenty of morphological variation. Long before molecular phylogenies, workers on Anolis, knew (or at least strongly suspected) that ecomorphs were not monophyletic. This does not necessitate splitting Anolis, but it distinguishes it from other cases that may be oversplit.

Unlike others, I don’t think that this fragmentation in usage is necessarily horrible because it will force anyone who works on this clade to consider phylogenetic relationships and to be cautious about applying any methods that blindly consider genera to be equivalent in any way (this includes any meta-analyses of squamates that use genera as a unit of measure).

In conclusion, even if I’m playing devil’s advocate to some degree, I have a real concern about the best way to encourage the use of phylogenetic information outside of research that is focused solely on taxonomy and the phylogenetic history itself.

KIRSTEN E. NICHOLSON, BRIAN I. CROTHER, CRAIG GUYER & JAY M. SAVAGE (2012). It is time for a new classification of anoles (Squamata: Dactyloidae). Zootaxa, 3477, 1-108

Nicholson, K.E., Glor, R.E., Kolbe, J.J., Larson, A., Hedges, S.B. & Losos, J.B. (2005) Mainland colonization by island lizards. Journal of Biogeography, 32, 929–938.

We’ve had a lot of great discussion about Nicholson’s et al.’s proposal to split Anolis into eight genera. To date, most of the commenters have been against the proposal; I’d like to explain why I agree with this majority view.

Anole Annals summarized the arguments for splitting Anolis several days ago. Nicholson et al. argue that the failure to divide Anolis in the past has inhibited evolutionary and systematic research:

“Systematic progress in this regard has been delayed by an extremely conservative taxonomic approach to recognizing the diversity within the group and its extraordinarily ancient historical roots.” (p.4)

“The current practice (following Poe, 2004) of treating all dactyloids as comprising a single genus underemphasizes the evolutionary diversity within the family (as currently recognized) and obfuscates major biological differences among clades. In addition, simply because of the large size of the family (nearly 400 valid species), the single genus concept can be a hindrance to scientific communication regarding evolutionary events and directions of future research.” (p.13)

These quotes suggest that research on anoles is being held back by treating the entire clade as a single genus, but where is the evidence for these claims? No examples are provided. Quite the contrary, research on anoles has flourished over the last several decades, making it a well-known group for the study of many diverse evolutionary phenomena, and much of this work has explicitly incorporated phylogenetic information. Indeed, anole evolution, considered in a phylogenetic context, has become a commonly cited textbook example of adaptive radiation, and work on anoles has become so broad and deep that one commenter at last year’s Evolution meetings noted that “I didn’t go to the Evolution meetings for three years…When I “returned” in 2011 in Norman, it was like everybody had switched to working on anoles and sticklebacks!” The Dobzhansky Prize winners at the last two Evolution meetings have conducted phylogenetically-based research on anoles, and anole workers have nabbed the Fisher Prize and four Young Investigators Prizes at the meetings in that time span. Anole research is going gang-busters, and it is hard to see how retaining the name Anolis for the entire clade has had any sort of detrimental effect. (see also comments by Eric Schaad on why taxonomic names are no longer important for conducting phylogenetically-based evolutionary studies and by Yoel Stuart on why splitting evolutionarily-interesting clades may actually impede research).

I disagree with the proposal to split Anolis into eight genera for two reasons. First, it is not possible for the Linnean classification system to fully represent phylogenetic relationships—splitting genera simply changes the information conveyed, gaining some bits of information and losing others (for more discussion on this point, see the recent post by Luke Mahler and ensuing commentary). Second, splitting Anolis will be extremely disruptive for scientific researchers and the public.

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A half century ago my graduate research was stimulated and influenced by the important unpublished Etheridgean thesis (Etheridge, “1959”, 1960).  As an E.E. Williams student, I was an  adopter, user, and later coiner of informal names for seemingly natural evolutionary groups in the diverse genus Anolis.  In most cases, I was building upon (sometimes tweaking) the foundation of Etheridge’s classification.  I believed then and believe now that the use of informal names for natural groups worked well for communicating evolutionary hypotheses both to specialists in our field, and to a broader audience of professional and amateur biologists who are likely not well informed about the nomenclatural history of these lizards.

Nicholson et al. (2012) believe otherwise. Here is their overview, page 13:

“The role of systematics is to advance our understanding of biological diversity in the natural world. Its practitioners are the guardians of the knowledge produced by past generations and responsible for the rational interpretation of new data and their implications. Within this framework, phylogenetic inference has consequences that we think bind its practitioners to produce a systematic classification of the studied organisms. Such a classification must be founded on the inferred evolutionary relationships and dictated by the canon of monophyly.”

I support that.

This note, then, is neither about the role of systematics, nor the  interpretation of phylogenetic analyses (the Nicholson et al. presentation is comprehensive and extremely valuable).  Rather it concerns their conclusion to the cited paragraph about the use of Anolis, as the generic name for the entire clade. They write:

“the single genus concept can be a hindrance to scientific communication regarding evolutionary events and directions of future research.”

I believe exactly the opposite. Specifically, I believe that the single genus concept enhances scientific communication and suggests directions of future research.

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We’ve already had lots of discussion about Nicholson et al.’s (2012) recent proposal that Anolis be fragmented into eight genera.  Throughout the course of this discussion, several posts and comments have suggested that anole biologists might be compelled to implement Nicholson et al.’s proposed generic revision by the International Committee on Zoological Nomenclature (ICZN) and its rules for nomenclature (a.k.a. the ICZN* or The Code) (see comments on recent posts by Losos and Sanger).

Although I must admit at the outset that I am not an authority on The Code or its implementation, I will argue below that the belief that the code compels anole biologists to accept Nicholson et al.’s proposed taxonomic revision is completely false.  The ICZN has neither the authority, nor the interest in, policing taxonomic practice and will have no role in determining whether Nicholson et al.’s (2012) new generic classification is accepted or rejected by the community of researchers who study anoles.  I believe that the reasons for this are fairly straightforward and uncontroversial, but they do require us to think a little about our taxonomic philosophy and the difference between taxonomy and nomenclature.

Let’s start with some basics for the non-systematists.  According to the ICZN, the goal of taxonomy is “the identification and interpretation of natural groups of organisms (i.e., taxa) based on characters (such as morphology, genetics, behaviour, ecology).”  One piece of good news for anole biology is that everyone involved in debate over Nicholson et al.’s new classification shares the same fundamental taxonomic philosophy – namely, that taxa should be diagnosed using phylogenetic trees and should correspond with monophyletic groups.  We may debate whether certain taxa are supported as monophyletic by the available data, but we all agree that recognition of monophyletic groups is a primary objective of any taxonomic scheme for anoles.

More good news: The Code has no interest in getting involved with taxonomic decisions.  I realize that the The Code can be really boring to read, but you don’t have to read more than the first two paragraphs of the introduction to get this message (in a few cases I’ve added my own emphasis by bolding text):

“The 4th edition of the International Code of Zoological Nomenclature … has one fundamental aim, which is to provide the maximum universality and continuity in the scientific names of animals compatible with the freedom of scientists to classify animals according to taxonomic judgments.  The Code consists of Articles … [that] are designed to enable zoologists to arrive at names for taxa that are correct under particular taxonomic circumstances. The use of the Code enables a zoologist to determine the valid name for a taxon to which an animal belongs … There are certain underlying principles upon which the Code is based. These are as follows: (1) The Code refrains from infringing upon taxonomic judgment, which must not be made subject to regulation or restraint…”

Rather than concerning itself with taxonomy, which inevitably involves subjective decisions made by systematists that specialize on particular groups of organisms, The Code focuses exclusively on nomenclature, or “the system of scientific names for taxa (such as species, genera, or families) and the rules and conventions for the formation, treatment, and use of those names.”  The Code, therefore, merely provides “a set of rules for the naming of taxa that follows an internationally agreed, quasi-legal procedure.”

With this background, we can return to a consideration of Nicholson et al.’s classification and the role that The Code may have in its implementation.  Nicholson et al. argue that in order to appreciate and study the phylogenetic diversity of anoles we must formally recognize the taxon that includes all anoles not as a single genus, but rather as a number of related genera.  Although determining whether to proceed with the traditional classification involving a single genus or the Nicholson et al. classification that recognizes eight genera might seem to be a distinction between two alternative systems of nomenclature whose outcome is dictated by the The Code, this is not the case.  Instead, both alternatives are perfectly compatible with The Code, and the decision about which classification to adopt moving forward is a subjective taxonomic decision that must be made by the community of biologists who study anoles.

All The Code says is that if we anole biologists want to recognize the taxa that Nicholson et al. have diagnosed as genera, we must use the names they have resurrected from the historical literature and applied to these taxa.  If I wrote a paper tomorrow that gave a new generic epithet to the same taxon that Nicholson et al. have named Ctenonotus, this new name would be rejected under the rules of priority outlined in The Code.  However, The Code respects the right of anole biologists to make the subjective taxonomic decision about whether we want to recognize the taxa diagnosed by Nicholson et al. as genera, or instead recognized them informally as series or species groups, as anole biologists have done for decades.  Recall from our earlier passage from The Code that its rules for nomenclature only apply “under particular taxonomic circumstances.”

My fellow anole biologists, we have a taxonomic decision to make and the ICZN is not going to make it for us.  It seems that the worst outcome would be fragmentation of the community of anole biologists, with some researchers using the traditional approach and others applying Nicholson et al.’s revised generic classification.  More readings and notes are after the fold.

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In our comparison of mainland and island species turnover, we sampled mainland communities by randomly superimposing each of the Caribbean islands on the mainland five times. In each of these mainland island-shaped regions, we then tallied how many species were present and then measured turnover between regions.

Oceanic islands are famous for their high endemism. We all love Darwin’s finches, Hawaiian honeycreepers, Komodo Dragons, and all those weird things on Australia. These endemic wonders suggest that islands may be home to unique processes of diversification.  However, there are many mainland regions that rival islands in their level of endemicity, especially in mountainous regions that have strong dispersal barriers and environmental gradients. Thus, you could ask, are islands truly special?

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