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Higher taxonomy and progress

Comments on taxonomy related to version 6.0:

In the last year (2013) there has been considerable progress in the functioning of the database and addition of species. My comments on version 5.6 remain in force. Changes in 2013 seem to have mostly been in the naming of species, although there are some big changes looming. The largest questions in amphibian systematics that I can think of are: 1) resolution of the phylogeny and taxonomy of Megophryidae (at the moment mostly a fabric of A and not-A groups); 2) resolution of tropical Asian ranoids, particularly Ranidae (this will be an enormous task because relatively few of the species have been named); 3) teasing apart the mess which is Hyperolius in central Africa, although some people are doing the heavy lifting, without fanfare, that resolution of this problem requires. After those three giant issues, there are many taxonomic and phylogenetic issues, mostly in tropical Asia but also in tropical Africa that demand attention. And, of course, there is the issues of resolving the microhyloid groups worldwide and the arciferal families of southern South America. These are going to be tough problems to be resolved although there have been some relatively superficial treatments that are pointing the way towards resolution. Fortunately for those of us who watch global developments the size and impact of international collaborations are really starting to bear fruit.  

Comments on taxonomy related to version 5.6: 

"What gets us into trouble is not what we don't know. It's what we know for sure [e.g., assumptions of analysis or the inerrancy of particular characters for recovering phylogeny] that just ain't so."—Anonymous, but usually attributed to Mark Twain

The last 22 months (most of 2011 and all of 2012) since the last version (version 5.5) went online have been by turns exciting, annoying, and discouraging. One issue was that due to big personnel changes at the AMNH getting a new version online was extraordinarily difficult. But, thanks to Matt Tarr of the Digital Department, with generous support from Catherine Devine (Chief Digital Officer) and Ann Canty (Sr Vice President of Communications) we succeeded. My sense of discouragement was more general and focused on the fact that the United States National Science Foundation (NSF) continues in its direction of promoting science as story-telling, impressive technicalities, and "food security" as over-arching optimality criteria for support of science. This at a time when the only part of the world that has not had its amphibian fauna largely erased by chytrid fungus but is also the least known part of the globe with respect to amphibian diversity and species: Southeast Asia. This evolution in NSF priorities has been detrimental to an adequate understanding of world biodiversity, right at the time we are going over the biodiversity cliff. But, of course, NSF understands better than we who their audience is, which is Congress, and their function, which is getting overhead money to the colleges and universities in a way politically acceptable to that body. The brighter news which lessens the sting somewhat is that Brazil and China have stepped up and are funding biodiversity science in a big way, the result being that they are rapidly eclipsing the USA as centers of herpetological biodiversity studies. Nevertheless, it was an interesting year for publication, especially for someone who is interested in the normative aspects of science. More than any time in the past I see propaganda and dysinformation campaigns passing as the state of evidence and scientific inference, especially online, but not limited to that medium (see below). Had I not been able to guess the source(s) I would have come to the conclusion that what I read in Wikipedia and Wikispecies regarding amphibian taxonomy was generated by Fox News. Having said that, there were some definite scientific highlights.

Pyron and Wiens (2011): The very large molecular study by Pyron and Wiens (2011) based on the increasingly enormous number of legacy Genbank DNA sequences is obviously the biggest news during the 2011-2012 interim period. As a matter of course, the AMNH workgroup here and other colleagues around the world reanalyzed the Pyron and Wiens dataset and found, happily, that using their software, analytic method, and dataset we/they could not find a more optimal tree. This means that I am accepting this tree for purposes of this catalog at face value (with issues noted below), although readers should note the ironic absence from the dataset of any morphology (especially data from the remarkable larval study of Haas, 2003) given Wiens' (2007) previous exceedingly strong words on the importance of morphology to understanding amphibian systematics. There is also the puzzling exclusion by Pyron and Wiens of considerable amounts of available Genbank data for the loci the authors suggested they included as a matter of course, such as most of the rhodopsin data from Faivovich et al.'s (2005) study of hylid relationships. Unfortunately, the study includes Genbank sequences that were previously noted to be misidentified. For examples that became evident due to the surprising placement of terminals in their tree, Poyntonophrynus vertebralis sequences included by Pyron and Wiens were reidentified as Amietophrynus maculatus by Cunningham and Cherry (2004); sequences associated with Yunganastes pluvicanorus in the Frost et al. (2006) study and reused by Pyron and Wiens were reidentifed as Pristimantis pharangobates by Padial (2007); the 12S and 16S sequences of Amolops daorum were reidentified as Odorrana hmongorum by Stuart et al. (2010). I did not attempt to verify all of the sequences for taxa whose position did not jump out at me as problematics, but this is something that must happen before more progress takes place. Moreover, the authors apparently lack basic familiarity with the rules of zoological nomenclature. Their new names Paratelmatobiinae and Pristimantinae are invalid nomina nuda under the International Code of Zoological Nomenclature (1999) for reason of failing to present (Art. 13.1.1) "a description or definition that states in words characters that are purported to differentiate the taxon". As a result of these problems this paper presented me with something of a quandary. Should I ignore this paper, as recommended by several colleagues whose work was impacted by the Pyron and Wiens analysis, to wait for a study evidencing more care in the construction of the dataset? No; there are few analytical problems in this study to which any large study is not heir so that would put me on a slippery slope. Moreover, there is no doubt that Pyron and Wiens (2011) intended the effort to be taken seriously, and they provided a number of novel hypotheses of relationship that invite further scrutiny. For example, their rejection of Hemiphractidae as the sister taxon of the brachycephaloid families (Terrarana), previously suggested by Heinicke et al. (2009), has interesting implications about the evolution of frog life-history strategies. And, although I agree in the sense of descriptive efficiency with J. J. Wiens about the impact of missing data (e.g., Wiens and Morrill, 2011), analysis of datasets with such enormous amounts of missing data (> 80% in this case) are controversial more-or-less universally (see, e.g., Kearney, 2002; Kearney and Clark, 2003; Lemmon et al., 2009; Simmons, 2011). The result is that progress to be believed by the systematics community will have to include a lot of new sequencing as well as smaller, more-densely-sampled studies to corroborate regional tree structure. There remain issues that must be addressed by subsequent studies and much denser datasets, such as the low support values in critical areas of the tree. And, because missing data alone improve maximum-likelihood scores (Denton and Wheeler, 2012) there are good reasons to increase not only taxon sampling but data density as well. Nevertheless, this study is a jumping-off point for additional studies based on a more carefully-assembled and denser data sets. So, as mentioned above, I have accepted the tree and family-level taxonomic novelties of Pyron and Wiens for purposes of this catalogue, except for a few places where the results may/probably rest on misidentified Genbank sequences (e.g., some alsodines, some Amolops, and some bufonids), all detailed in the accounts and in the legends of the comparison bufonid and ranid taxonomy provided in figures below. In addition, published too late for exclusion by Pyron and Wiens, sequence AY880507, nominally Aquixalus odontotarsus, and AY880503, nominally Kurixalus carinensis, were implied by Rowley et al. (2011) to be misidentified or at least requiring verification. And, some of the sequences for nominal "Bufo valliceps" employed by Pyron and Wiens and which apparently explains the novel placement of this taxon in their tree, are identifiable as Incilius leucomoyos, according to Mendelson and Mulcahy (2011). These corrections are included here not as a criticism of Pyron and Wiens, but to point out that all of us who work on large studies are all subject to one degree or another to others' identifications of sequences submitted to Genbank.

Family-group changes reflected in version 5.6 that extend from the Pyron and Wiens study are: Ceratophryidae and Cycloramphidae of version 5.5 are reformulated into Alsodidae, Batrachylidae, Ceratophryidae, Odontophrynidae, Rhinodermatidae, and Telmatobiidae. Former Leiuperidae is treated as a subfamily of Leptodactylidae along with Leptodactylinae and the nomen nudum Paratelmatobiinae (employed here because I did not know what else to do). Strabomantidae is submerged in pieces into Craugastoridae. I expect that these taxa will remain unstable in various permutations for some time as we learn more about them.

What I have not adopted is Pyron and Wiens' recommended generic taxonomy, which they apparently took directly from AmphibiaWeb, an online database that is primarily focused on amphibian conservation and public outreach, which although it styles iself "the place for accurate, vetted information on amphibians," (D.B. Wake in R. Sanders, U.C. Berkeley news release of 30 July 2012), presumably referencing its aggregator function of mirroring the content of several other vetted websites such as iNaturalist, the IUCN Redlist, Genbank, and ASW, at least in the recent past it employed a non-transparent taxonomy that purposely lagged well behind the rapidly evolving state of the literature of amphibian taxonomy for the stated reason of trying to maintain nomenclatural stability, although this has resulted in just the nomenclatural confusion the keepers of this site claimed they hoped to avoid. (Note, however, that as of 27 July 2012, the generic taxonomy of bufonids and ranids in AmphibiaWeb was updated to reflect the progress of the last 6 years, although the AW taxonomy is still not completely in touch with the state of the literature.) As a result of this adoption of the AmphibiaWeb taxonomy by Pyron and Wiens, their preferred generic taxonomy is wildly inconsistent with their own tree and  deeply at variance with the state of understanding at that time, which is reflected in the fact that the Pyron and Wiens tree is almost completely consistent with the taxonomy employed in version 5.5 of Amphibian Species of the World (2011), which was certainly available to Pyron and Wiens prior to submission of their manuscript, and deeply inconsistent with the generic taxonomy they recommended. Why systematists in 2011, particularly two with pretensions of leadership, would embrace a non-monophyletic taxonomy in preference to an existing monophyletic one is an open question. Pretty clearly one has to look for Pyron and Wiens' motives in this adoption somewhere other than science, although given the tone of Wiens' (2007; see the response by Frost et al., 2008) earlier paper, it's obvious he followed his own earlier advice. For examples of how the Pyron and Wiens tree (manuscript submitted to MPE on 7 May 2011; version 5.5 of ASW went live on 31 January 2011) largely confirms the taxonomy that existed in early 2011 as the state of the literature and rejects their own preferred taxonomy, I have provided their own bufonid and ranid tree figures, with their preferred taxonomy in the left column (their tree terminal labels)—the taxonomy straight out of AmphibiaWeb at the time—and the generic taxonomy in the right column from ASW version 5.5 (available when the Pyron and Wiens' manuscript was written). See downloadable pdf (readable by Adobe Reader vers. 8 and later) figures: Bufonidae 1, Bufonidae 2, Ranidae 1, and Ranidae 2. In addition, one has to wonder why various nomenclatural actions were taken by Pyron and Wiens without discussion: 1) See Blotto et al. (2012) for wonderment at the lack of discussion of the substantial counter-evidence to their molecular tree of alsodids and their taxonomic changes within that group, which turn out to be based on misidentified sequences; 2) instances (e.g., the transfer of Ikakogi from incertae sedis within Centrolenidae into Centroleninae) where taxonomic changes were made by Pyron and Wiens on the basis of less evidence and fewer terminals than the earlier work (e.g., Guayasamin et al., 2008) that had resulted in the pre-existing taxonomy; 3) And other undocumented changes, like their association of Adelastes, Altigius, Arcovomer, Hyophryne, Melanophryne, Myersiella, Relictovomer, Stereocyclops, and Syncope with Gastrophryninae (Microhylidae) on the basis of no data or discussion whatsoever (unless we look to the uncredited and unpublished dissertation of Eli Greenbaum). As a tree-building exercise this work is competent. As a contribution to systematics and science generally it suffers from not remotely meeting the bar that Wiens set for himself in 2007.

Wilkinson et al. (2011), Kamei et al. (2012), and San Mauro et al. (2012): The other major changes are the delimitation of several new caecilian families by Wilkinson et al. (2011) as well as the new family provided by Kamei et al. (2012). With these papers, we really begin to see coming into focus the global and antique biogeography of a very ancient group of amphibians that has not enjoyed the attention that it deserves. These authors deserve at least a free round of beers.

Blackburn and Wake (2011) and Age-Equivalency of Taxonomic Ranks (Time-trees): A brief review of higher taxonomy of amphibians and, more importantly, the disposition of fossils (not treated in ASW) was presented by Blackburn and Wake (2011). But, they were critical of ASW (this section likely written by D.B. Wake as it dealt with salamanders) for not recognizing Dicamptodontidae (i.e., Dicamptodon) as distinct from Ambystomatidae (i.e., Ambystoma) on the basis of their "substantial biological differences" (i.e., their different spinal nerve patterns, apparently) and, more pointedly, because of their mutual antiquity, while these authors were otherwise inconsistent in their application of a time criterion, which they implied was sufficient evidence for Linnaean rank. I am easy-going when it comes to ranks and changing them because I see Linnaean rank as utilitarian, a useful memory device that is a vestige of pre-phylogenetic systematics that allows us to bring a focus on particular phylogenetic questions and to render for discussion convenient chunks of the genealogical nexus. But when ranks are treated as if they are elements of scientific theories, or worse, as natural classes, I take exception, particularly when the authors asserting this are inconsistent in their own application.

Linnaean ranks (e.g., orders, families, genera), with the arguable exception of taxonomic species (which are almost always larger than the items delimited by the interface of phylogenetics and population genetics), have no objective reality as natural classes of comparable individuals (Hennig, 1966), but, regardless of this inarguable fact, there has been some effort in recent years to try to give coordinate ranks to taxa that are more-or-less of coordinate age. Athough generally harmless, this activity has hardly appealed to any rigorous scientific principle or objective criterion that I can identify, instead generally resting on subjective pre-evolutionary impressions of similarity and difference or simply tradition. Hennig (1966: 184-193) noted that one basic problem in the application of time-criteria to ranks is that there are many more time periods (infinitely many more, I would suppose) than there are taxonomic ranks. Hennig's solution, offered explicitly in the sense of a political compromise between optimizing on age of origin and trying to preserve familiar ranks (mostly coined in a pre-phylogenetic framework of subjective estimates of morphological similarity) was for different major groups to have their internal taxonomies optimized on different rank-time equivalencies, thereby preserving as much as possible the taxonomies with which people are familiar. In other words and as an example, he was attempting to come up with an approach that would allow ranks to imply age of origin, at least within taxonomic neighborhoods, while preventing Amphibia from becoming (at best) a genus in Craniata. Another solution is to forego ranks completely, a position cogently argued by de Queiroz and Gauthier (1990, 1992, 1994). There is no theoretical bar to rankless taxon names (essentially even by the International Code of Zoological Nomenclature, 1999, which only regulates family-group, genus-group, and species-group taxon names) which provides relief to the problem of there being more taxonomic levels than ranks, but the practical counter-issue is the mnemonic ease of a consensual and arbitrary set of ranked groups that help with the organization of inventories, collections, and the like—a system (ca. "method of loci"; http://en.wikipedia.org/wiki/Method_of_loci) that lends itself to how memory works but which lacks any scientific underpinning for rank equivalencies. For this reason of memory utility (I think) rankless taxonomies have not made big inroads into the part of the professional systematics community that is actually doing taxonomic revisions. What has evolved in professional practice is a system where unranked taxon names (like Sauropsida) are attached to large taxa that contain other unranked (e.g., Aves and Crocodylia) and ranked taxa (like Struthionidae and Crocodylidae), in part as suggested by de Queiroz and Gauthier. This hybrid approach, where taxon names above the level of family-group are treated as unranked and family-group and down are ranked, seems to have reduced many of the problems perceived by taxonomists by allowing traditional familial (ranked) taxonomies to be retained. The upshot is that at this point very few systematists, and fewer every year due to Max Planck's observation that the salutary frequency of funerals enhances scientific progress, thinks of any taxon name above the level of family as having any particular rank attached to them. One no longer sees arguments beyond a few fringe authors over, for example, whether Serpentes is a suborder or infraorder. Calling Aves a class requires such groups as Crocodilia to be classes as well, with lots of Linnean nomenclatural gymnastics to preserve other familiar taxonomic names. But, if Aves is just a rankless proper name it can be tied into Sauropsida and preserve the family-group nomenclature that ornithologists use routinely for communication. At least that is how the situation looks to me that has allowed traditions of familiar nomenclature to be more-or-less maintained.

Nevertheless, what seems to be happening in amphibian systematics is that age of origin appears to be gaining traction as a criterion for assignment of ranks, at least to family-rank (and not genera, at least so far) concomitant with the increasing popularity of various molecular methods for estimating age of divergence. My guess is that this will be a valiant failure for all of the same problems detailed 46 years ago by Hennig (1966) unless rank-specific time criteria are agreed-upon by pact and applied consistently. (But because those criteria are always going to be arbitrary, I do not expect much agreement on this front, the same problem that phenetics had with applying a numerical value to general similarity.) At the moment the argument of taxon age is used by many workers not scientifically but as a rhetorical device for special pleading (such as Blackburn and Wake's arguing for family rank for Dicamptodon), without having ever seriously addressed the relevant optimality criterion.

Within salamanders, Blackburn and Wake (2011) apparently followed the time-tree and classification of Vieites et al. (2009), although this renders logical inconsistencies due to that latter study not including terminal taxa that would have rendered a clearer appreciation of "family" ages than is apparent in that paper. (A single representative of a family cannot show any divergences within the "family", regardless of its age of divergence from its sister taxon.) Blackburn and Wake (2011) argue for Dicamptodontidae as a separate family from Ambystomatidae on the basis of its long-term recognition (since 1976 in some circles), its purported "biological" distinctiveness (in the eye of the beholder, apparently; they look like ambystomatids to me), although the separation of Dicamptodon plus Rhyacotriton from Ambystomatidae by Edwards (1976), a student of Wake's, rested on the belief that Dicamptodon and Rhyacotriton were nearest relatives and together far from Ambystoma, although the sister-taxon status of Ambystoma and Dicamptodon was subsequently documented by Larson (1991), another student of Wake's, and by Good and Wake (1992). Estes (1981), who did recognize Dicamptodontidae (but in the earlier sense of including Rhyacotriton), assigned a number of former ambystomatid fossil taxa to Dicamptodontidae (sensu lato), this action considered relevant by Blackburn and Wake, even though Milner (2000) and Gao and Shubin (2012) noted that all of these fossil taxa, except for Paleocene Dicamptodon (Naylor and Fox, 1993), are now considered enigmatic and of a uncertain taxonomic assignment. (The authors could have profitably looked at the wonderful website/database Lisanfos KMS [http://www.lisanfos.mncn.csic.es/?module=searches] maintained by Borja Sanchiz and Carolina Martín.) Frost et al. (2006) returned Dicamptodon to Ambystomatidae, where it had resided prior to 1976, because there was no phylogenetic reason to do otherwise; no one looking at the preponderance of all evidence disagrees that Ambystoma is the sister taxon of Dicamptodon among living taxa (although morphology [Gao and Shubin, 2012] continues to suggest that Rhyacotriton is the sister of Dicamptodon, together forming the original content of Dicamptodontidae of Edwards, 1976, an arrangement that is not endorsed by Blackburn and Wake, 2011). Blackburn and Wake (2011) argued that the return by Frost et al. (2006) of Dicamptodon to Ambystomatidae was inappropriate due to "substantial biological differences" (the spinal nerve pattern, I guess, unless "biological" means something else in this instance) between Ambystoma and Dicamptodon, because of fossils that no one else thinks are associable with Dicamptodon, and, more pointedly, because of the estimated 100 million year divergence time of Dicampton and Ambystoma. With respect to the "substantial biological differences" this seems strange to accept with respect to the biological diversity within its sister taxon, Ambystoma. Is this just about spinal nerve patterns, or are they really saying that Ambystoma dumerilii is more like A. cingulatum "biologically" than A. cingulatum is like Dicamptodon? And if not just a slogan, how would "biological differences" be measured without falling into the same trap of authoritarian subjectivity that killed phenetics and evolutionary systematics as scientific approaches?

But, let us look seriously at the time-rank criterion, since the science of systematics is (or, at least, should be) all about transparent optimality criteria. If one applies a time criterion to a taxon rank, there has to be an upper and a lower bound for assignment of that rank, at least for families because they have categories like subfamilies below them and superfamilies above that one would assume would have to comply with a time criterion as well. But, if you look for application of the 100 mybp optimality criterion in the rest of the Blackburn and Wake's salamander taxonomy you can see that this claim of divergence time being critical was just a rhetorical device, not an optimality criterion. Vieites et al. (2009) did not address the genera within Hynobiidae, although Zhang and Wake (2009) did, so David Wake had to be familiar with the antiquity and "substantial biological difference" of Onychodactylus from other hynobiids. And, if the 100 mybp criterion is applied rigorously to Hynobiidae it requires familial recognition of Onychodactylus from the remainder of Hynobiidae, an action not taken by Blackburn and Wake (2011). Also, Necturus and Proteus must be considered distinct families (considered coordinate subfamilies by Blackburn and Wake, 2011, suggesting that however they are applying their time criterion, it allows some salamander subfamilies to be older than some salamander families), and, if we take the error estimates in Zhang and Wake (2009) seriously, the divergence of the salamandrid subfamilies Pleurodelinae and Salamandrinae are estimated to be ca. 96 mybp (+/–; several million years) so one would think that this would be within the error estimates of a family distinction as well. Does the argument that Dicamptodontidae be recognized on the basis of its antiquity appear to be an application of a scientific optimality criterion?: no. What it looks like is appealing to age of divergence as a debating device to bolster acceptance of the monogeneric Dicamptodontidae, isolated from consideration of other more-or-less identical situations—a practice widely referred to as lawyering, not science.

Comments on taxonomy related to Version 5.5

With the appearance of six publications (Chippindale et al., 2004; Faivovich et al., 2005; Macey, 2005; Frost et al., 2006; Grant et al., 2006; and Roelants et al., 2007), amphibian systematics moved substantially towards a taxonomy consistent with evolutionary relationships. Concomitantly, we entered a period of nomenclatural instability in which workers will rush to tie up all of the loose ends that are no longer concealed by nonmonophyletic groupings (e.g., the older senses of Pseudoeurycea, Plethodontinae, Bufo, Hyla, Hyperoliidae, Leptodactylidae, Eleutherodactylinae, Rana, Hylarana, Ranidae, Microhylidae, and Caeciliinae). Because taxonomic stability must be an artifact of understanding, not authoritarian decree, I think this instability reflects the health of amphibian systematics as a scientific endeavor driven by evidence and not something that makes systematics a "laughingstock" of science (Wake, 2006 [cf. Sokal and Sneath, 1963]; for more scientific views of this issue see Dominguez and Wheeler, 1997, and Grant and Kluge, 2005). Adherence to nonevolutionary/nonmonophyletic groups by social compact would be quaintly anachronistic were it not such a threat to progress in systematics research.

Over the next several years there will be considerable discussion of the higher taxonomy of amphibians. This will include nomenclatural discussions of how best to name evolutionary groups as well as more important discussions of epistemology, evidence, and analytical methods as they impact inferential biology. Throughout the ensuing debate, it will be important to distinguish legitimate scientific disagreements grounded in evidence and analysis from authoritarian posturing based only on opinion and deference to tradition and social conservativeness. This kind of resistance will rest largely on the political propaganda and innuendo that unfortunately so infects amphibian systematics. Nevertheless, what should come out of the scientific exercises associated with the controversies is a huge increase in the amount of evidence and the number of explicitly tested phylogenetic hypotheses, as well as more philosophically rigorous discussions of analytical methods and their underlying justifications.

Even though I have been part of this push towards monophyly in amphibian taxonomy, my ongoing objective is to continue to update ASW as evidence accumulates and the current phylogenetic hypotheses (e.g., Chippindale et al., 2004; Faivovich et al., 2005; Macey, 2005; Frost et al., 2006; and Grant et al., 2006) are refined or refuted by additional evidence (e.g., Che et al., 2007; Li et al., 2008; Biju and Bossuyt, 2009; Van Bocxlaer et al., 2009). My intention is to continue to give new ideas and nomenclatural novelties an airing, to let this online catalog support change and the younger workers who make systematics the dynamic field that it is.

A comparison of the family-group names applied in ASW versions 3.0 (the old days) and 5.4 (a continuation of the post-version-4.0 new days) provides a general road-map for the number of changes in amphibian taxonomy made in the recent past.

 

Version 3.0 (2004) families and subfamilies Version 5.4 (2010) families and subfamilies Notes and explanations
Anura    
Allophrynidae Allophrynidae Placed as a subfamily of Centrolenidae by Frost et al., 2006, to reflect the sister taxon relationship of Allophryne ruthveni with the traditional Centrolenidae. Guayasamin and Trueb, 2007, and Guayasamin et al., 2009, disputed the rank of this taxon as a subfamily of Centrolenidae, although they concurred with its placement as the sister taxon of Centroleninae, and continued the recognition of the monotypic family, Allophrynidae. Although the two arrangements reflect the same phylogeny DRF follows this taxonomy because it reflects the preference of the majority of those who are actively working on centrolenids.
Arthroleptidae Arthroleptini (roughly) of Arthroleptidae: Arthroleptinae Frost et al., 2006, placed former Arthroleptidae, Astylosternidae, and Leptopelinae (formerly in Hyperoliidae) into a reformulated Arthroleptidae, containing two subfamilies Arthroleptinae (for former Arthroleptidae [sensu stricto] and Astylosternidaee) and Leptopelinae (for a taxon formerly attached to Hyperoliidae).
Ascaphidae Leiopelmatidae Frost et al., 2006, returned Ascaphus to Leiopelmatidae to reflect the sister-taxon relationship of Ascaphus and Leiopelma.
Astylosternidae Arthroleptidae: Arthroleptinae See comment under Arthroleptidae.
Bombinatoridae Bombinatoridae  
Brachycephalidae

Brachycephalidae,

Craugastoridae,

Eleutherodactylidae,

Strabomantidae

 

Frost et al., 2006,  following Dubois, 2005, severely modified the content of Brachycephalidae by the inclusion of the former Eleutherodactylinae. Heinicki et al., 2007, severely revised the generic concepts on the basis of molecular data. Hedges et al., 2008, subsequently partitioned the monophyletic group into four families 
Bufonidae Bufonidae Frost et al., 2006, rendered a number of generic rearrangements to render a monophyletic Bufo and to formulate a taxonomy that invites additional work. Most of these changes have been confirmed and supported by Van Bocxlaer et al., 2009; Van Bocxlaer et al., 2010
Centrolenidae Centrolenidae: Centroleninae See comment under Allophrynidae
Dendrobatidae Aromobatidae and Dendrobatidae Grant et al., 2006, rendered extensive changes to the generic taxonomy of former Dendrobatidae (now Dendrobatoidea) and considered it to be composed of sister families, Aromobatidae and Dendrobatidae. This taxonomy has been widely accepted with only some resistance (e.g., Santos et al., 2009).
Discoglossidae Alytidae Frost et al., 2006, used the name of priority for this taxon.
Heleophrynidae Heleophrynidae  
Hemisotidae Hemisotidae  
Hylidae: Hemiphractinae Hemiphractidae Darst and Cannatella, 2004; Faivovich et al., 2005, and Wiens et al., 2005, showed that Hemiphractinae was not in Hylidae. Frost et al., 2006, recognized former Hemiphractidae as three families phylogenetically distant from each other. Guayasamin et al., 2008, suggested that these three groups (Amphignathodontidae, Hemiphractidae, and Cryptobatrachidae) form a monophyletic group and recognized one family, for which Hemiphractidae is the oldest name.
Hylidae: Hylinae Hylinae: Hylinae Faivovich et al., 2005, rendered extensive generic changes to render a monophyletic taxonomy.
Hylidae: Pelodryadinae Hylinae: Pelodryadinae Frost et al., 2006, placed Cyclorana and Nyctimystes in the synonymy of Litoria to render a monophyletic taxonomy.
Hylidae: Phyllomedusinae Hylinae: Phyllomedusinae Faivovich et al., 2005, rendered generic changes to render a monophyletic taxonomy.
Hyperoliidae: Hyperoliinae Hyperoliidae Frost et al., 2006, rendered former Hyperoliinae as coextensive with Hyperoliidae by transfer of Leptopelinae to Arthroleptidae.
Hyperoliidae: Leptopelinae Arthroleptidae: Leptopelinae See comment under Arthroleptidae.
Leiopelmatidae Leiopelmatidae Frost et al., 2006, reincluded Ascaphidae in Leiopelmatidae.
Leptodactylidae: Ceratophryinae Ceratophryidae (part) and Cycloramphidae (part) Ceratophryini was transferred by Frost et al., 2006, to a reformulated Ceratophryidae; they also transferred Odontophrynini into a reformulated Cycloramphidae.
Leptodactylidae: Cycloramphinae Leptodactylidae (part), Hylodidae, and Cyclramphidae Frost et al., 2006, transferred Scythrophrys and Paratelmatobius into Leptodactylidae from former Cycloramphinae; their reformulated Cycloramphidae contained the remainder of the former Cycloramphinae + Rhinodermatidae + part of Telmatobiinae, except for Thoropa, which they placed in a new family, Thoropidae. Grant et al., 2006, recognized that Thoropidae is in Cycloramphidae, but excluded Hylodidae (Cycloramphidae: Hylodinae of Frost et al., 2006) from Cycloramphidae sensu Frost et al., 2006, to render a monophyletic taxonomy.
Leptodactylidae: Eleutherodactylinae Brachycephalidae (part) See comment under Brachycephalidae.
Leptodactylidae: Leptodactylinae Leptodactylidae (redelimited), Leiuperidae Frost et al., 2006, included the former cycloramphines Paratelmatobius and Scythrophrys in Leptodactylidae but otherwise treated former Leptodactylinae as  a family. Grant et al., 2006, showed that Leptodactylidae sensu Frost et al., 2006, is polyphyletic, composed to two families: Leptodactylidae (for Hydrolaetare,  Leptodactylus, Paratelmatobius, and Scythrophrys) and Leiuperidae (for Edalorhina, Engystomops, Eupemphix,  Physalameus, Pleurodema, Pseudopaludicola, and Somuncuria).
Leptodactylidae: Telmatobiinae Calyptocephalellidae, Ceratophryidae (part), Cycloramphidae (part) Frost et al., 2006, showed that former Telmatobiinae is polyphyletic, with one group (Calyptocephalellidae [Batrachophrynidae in their work]) most close to the myobatrachoids, another group (Telmatobius, Batrachyla, and Atelognathus) most closely related to former Ceratophryini in a reformulated Ceratophryidae, and another group (including Hylorina, Alsodes, and Eupsophus) in a reformulated Cycloramphinae. Aguilar and Pacheco, 2005, and Córdova and Descailleaux, 2005, demonstrated that Batrachophrynus is in Ceratophryidae, leaving the remainder of "Batrachophrynidae" as Calyptocephalellidae
Limnodynastidae Limnodynastidae (part) Frost et al., 2006, transferred Mixophyes from Limnodynastidae into Myobatrachidae.
Mantellidae: Boophinae Mantellidae: Boophinae  
Mantellidae: Laliostominae Mantellidae: Laliostominae Frost et al., 2006, considered Mantellinae and Laliostominae as tribes within a reformulated monophyletic Mantellinae. Glaw and Vences, 2006, provided an extensively reformulated Mantellidae and retained the three-subfamily arrangement without rejecting the evidence or tree of Frost et al., 2006.
Mantellidae: Mantellinae Mantellidae: Mantellinae See comment under Laliostominae.
Megophryidae Megophryidae  
Microhylidae: Asterophryinae Microhylidae: Asterophryinae Frost et al., 2006, placed Genyophryninae as a synonym of Asterophryinae to prevent the paraphyly of Genyophryninae.
Microhylidae: Brevicipitinae Brevicipitidae Frost et al., 2006, recognized Brevicipitidae as a family, phylogenetically distant from Microhylidae.
Microhylidae: Cophylinae Microhylidae: Cophylinae  
Microhylidae: Dyscophinae Microhylidae: Dyscophinae  
Microhylidae: Genyophryninae Microhylidae: Asterophryinae (part) See comment under Microhylidae: Asterophryinae.
Microhylidae: Melanobatrachinae Microhylidae: Melanobatrachinae Frost et al., 2006, retained Melanobatrachinae, but noted that its content will likely change substantially with additional work.
Microhylidae: Microhylinae Microhylidae (several incertae sedis genera), Microhylinae,  Gastrophryninae, Kalophryninae, Otophryninae Frost et al., 2006, demonstrated that former Microhylinae is polyphyletic. They recognized a monophyletic Microhylinae and Gastrophryninae, but excluded several genera from either subfamily and placed them incertae sedis at the level of Microhylidae. Kalophryninae retained for Kalophrynus and Otophryninae for Otophryne in this catalogue.
Microhylidae: Phrynomerinae Microhylidae (see comment) Frost et al., 2006, did not recognize Phrynomerinae for Phrynomantis to avoid monotypic taxa. Retained in this catalog.
Microhylidae: Scaphiophryninae Microhylidae: Scaphiophryninae (see comment) Frost et al., 2006, followed Haas, 2003, in excluding Paradoxophyla from this taxon, placing it incertae sedis within Microhylidae. Van der Meijden et al., 2007, subsequently showed Paradoxophyla to be a scaphiophrynine
Myobatrachidae Myobatrachidae (part) Frost et al., 2006, reformulated Myobatrachidae by placing Rheobatrachus and Mixophyes in this group. Roelants et al., 2007 suggested that Mixophyes is a limnodynastine; the jury is out on this. 
Nasikabatrachidae Nasikabatrachidae Frost et al., 2006, placed Nasikabatrachidae in Sooglossidae, although Roelants et al., 2007, continued its recognition.
Pelobatidae Pelobatidae  
Pelodytidae Pelodytidae  
Petropedetidae Petropedetidae (reformulated) and Ranixalidae Frost et al., 2006, reformulated Petropedetidae to exclude Phrynobatrachidae, and to include Conraua and Indirana. Roelants et al., 2007, on the basis of additional evidence removed Indirana to its own family, Ranixalidae
Pipidae: Dactylethrinae Pipidae (part) Frost et al., 2006, rejected subfamilies within Pipidae.
Pipidae: Pipinae Pipidae (part) See comment under Pipidae: Dactylethrinae.
Rhacophoridae: Buergeriinae Rhacophoridae: Buergeriinae  
Rhacophoridae: Rhacophorinae Rhacophoridae: Rhacophorinae  
Rheobatrachidae Myobatrachidae (part) Frost et al., 2006, placed Rheobatrachus in Myobatrachidae
Rhinodermatidae Cycloramphidae (part) Frost et al., 2006, placed Rhinodermatidae in a newly demarcated Cycloramphidae.
Rhinophrynidae Rhinophrynidae  
Scaphiopodidae Scaphiopodidae  
Sooglossidae Sooglossidae (part) See comment under Nasikabatrachidae.
Urodela Caudata Frost et al., 2006, explained the nomenclatural change.
Ambystomatidae Ambystomatidae (part) See comment under Dicamptodontidae.
Amphiumidae Amphiumidae  
Cryptobranchidae Cryptobranchidae  
Dicamptodontidae Ambystomatidae (part) Frost et al., 2006, replaced Dicamptodon as the sister taxon of Ambystoma, within Ambystomatidae.
Hynobiidae Hynobiidae  
Plethodontidae: Desmognathinae Plethodontidae: Plethodontinae (part) Chippindale et al., 2004, and Macey, 2005, provided a monophyletic taxonomy of Plethodontidae that does not resemble the older, nonevolutionary taxonomy.
Plethodontidae: Plethodontinae Plethodontidae: Bolitoglossinae, Plethodontidae: Hemidactyliinae, and Plethodontidae: Spelerpinae See comment under Plethodontidae; Desmognathinae.
Proteidae Proteidae  
Rhyacotritonidae Rhyacotritonidae  
Salamandridae Salamandridae: Salamandrinae, Salamandridae: Salamandrininae; Salamandridae: Pleurodelinae Frost et al., 2006, recognized two subfamilies within Salamandridae, but this was superseded by Roelants et al., 2007, who showed this to be incorrect. Dubois and Raffaëlli, 2009, subsequently proposed a three-subfamily arrangement
Sirenidae Sirenidae  
Gymnophiona Gymnophiona  
Caeciliidae: Caeciliinae Caeciliidae (part) Frost et al., 2006, rejected the use of Caeciliinae as paraphyletic.
Caeciliidae: Typhlonectinae Caeciliidae: Typhlonectinae  
Ichthyophiidae Ichthyophiidae See comment under Uraeotyphlidae.
Rhinatrematidae Rhinatrematidae  
Scolecomorphidae Caeciliidae: Scolecomorphinae Frost et al., 2006, placed Scolecomorphidae as a subfamily of Caeciliidae.
Uraeotyphlidae Ichthyophiidae (part) Frost et al., 2006, placed Uraeotyphlidae into the synonymy of Ichthyophiidae.

 

 

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