Title: Triassic stem caecilian supports dissorophoid origin of living amphibians
​Authors: B.T. Kligman, B.M. Gee, A.M. Marsh, S.J. Nesbitt, M.E. Smith, W.G. Parker, & M.R. Stocker
Journal: Nature
DOI: 10.1038/s41586-022-05646-5

General summary: The origin of modern amphibians (frogs/toads, salamanders/newts, caecilians), which are more often termed 'lissamphibians' by scientists to differentiate from the more ambiguous 'amphibians,' has long been a vexing problem. The three modern groups are remarkably morphologically disparate, which makes it hard to both confidently identify and conceive of the ancestral lissamphibian. Lissamphibians today are also relatively small, a pattern thought to have characterized much of their evolutionary history and also an attribute that predisposes their remains to not have been fossilized. Exacerbating this is the extremely poor record of caecilians, which, even today, are a rather cryptic group found only in the equatorial regions and that typically burrow, making them rather hard to observe. Burrowing animals, especially those that not only burrow but that spend much of their lives underground, also have a poor fossil record, which compounds the problems for caecilians. The first caecilian fossils were not even reported until 1972 (previous reports were a misidentifed catfish spine and a misidentified cephalopid, respectively), and to date, there are less than a dozen distinct occurrences of fossil caecilians known globally over an 180 million year interval.

In this study, led by my colleague and current Virginia Tech PhD student Ben Kligman, we report nearly 100 new specimens of the earliest known caecilian in the fossil record from a single Late Triassic site in Petrified Forest National Park, Arizona. Although no complete skulls or skeletons are known, numerous fragments preserve unequivocally diagnostic features found only in caecilians, such as a jaw comprised of largely fused elements that remain separate in other tetrapods and two rows of small teeth with a distinctive feature called pedicelly – a dividing zone at the mid-height of the tooth that often leads the tips to be lost during preservation. This occurrences pre-dates the previous oldest occurrence of caecilians by at least 35 million years and provides new insights into the early stages of the group's evolution. In particular, the new fossils appear to capture the transition toward the modern caecilian condition in which there is extensive co-ossification of multiple elements to form a more consolidated skull (good for burrowing). Their occurrence in Arizona, which was positioned close to the equator in the Late Triassic, suggests that an origin within the equatorial belt also constrained their dispersal, therein offering an explanation as to why caecilians remain tied to these regions when frogs and salamanders have nearly a global distribution except at the poles (and Australia for salamanders).

Elucidating the evolutionary origin of highly specialized organisms has been a persistent challenge for evolutionary biologists and paleontologists because the patchy fossil record often obscures the gradual transition from a generalized "ancestral" form to the observed specialized one. Fossils that fill in these gaps, often dubbed "transitional fossils," contribute substantive information by their mixture of features, but it is not as if one can simply declare, "today I will find this transitional fossil" and then actually do so. For this reason, the evolutionary origins of various groups of living tetrapods like turtles and snakes has remained contentious to even the present day; we simply lack enough transitional fossils or cannot be certain that a given fossil truly represents a transition, rather than a convergence on a similar body plan (e.g., a long body with greatly reduced or entirely absent limbs occurs across many different groups of animals, not just snakes). It's only within my parents' lifetime that the notion that birds descended from dinosaurs became the accepted consensus, which today's 5-year-olds know by heart.

One of the most vexing origin stories is that of modern amphibians, collectively termed "lissamphibians." There are three living groups of lissamphibians: the worm-like caecilians, which are poorly-known to scientists and the public alike; frogs (of which toads are a subset); and salamanders (of which newts are a subset). The simple explanation for the ongoing uncertainty is how different these three groups look – one has entirely lost its limbs, another has lost its tail and shortened its body; and the third looks like a prototypical tetrapod (salamanders are often confused for lizards because people don't think amphibians have tails). As a result, it is difficult to figure out what a transitional form to one or all three would look like – does the common ancestor of these three groups have a long or short body, a tail or no tail, etc.

Both fossil and modern amphibians are on the smaller side of the tetrapod scale; consider that the recent capture of the new recordholder for the largest living toad (who was promptly euthanized due to being an invasive species in Australia) was for a cane toad weighing just under 6 lbs, or roughly equivalent to a large chihuahua (the healthy ones, not those severely obese ones you see in kitschy Route 66 hotels sometimes). Their skeleton is rather fragile, and in early stages of life (e.g., the tadpole stage of frogs), has not even solidifed into bone. This makes them poor candidates for fossilization, which is why the fossil record of caecilians and frogs is atrocious; salamanders benefit only from apparently taking up residence in the  lakes that lended themselves to lagerstätte like in the Jurassic of China. However, whereas salamanders and frogs become increasingly well-documented towards the present-day, caecilians remain nearly invisible in the fossil record.

It is no exaggeration to say that among the various groups of living tetrapods, caecilians have one of the worst fossil records. There are fewer than a dozen definitive occurrences of fossil caecilians between the Early Jurassic and the present day, fewer than 10 of which have been published in full. Until 1972, there were no published records of fossil caecilians from even recent history. The below summary figure showing the temporal distribution of published fossil caecilian records. Six of the nine records shown here are just vertebrae, and only Eocaecilia micropodia, known from several dozen specimens on the Navajo Nation of Arizona, is represented by any appreciable number of specimens.

The fossil record of caecilians likely owes to a combination of a lot paleobiological attributes that are all disadvantageous for their preservation. As discussed above, the small size of lissamphibians reduces their odds of being preserved. Where caecilians differ from most other lissamphibians is that they are fossorial, meaning they live underground (e.g., within leaf litter or soil) by burrowing with their heads (they have no limbs to speak of). If their extinct relatives had similar ecologies, which seems likely given the many skeletal adaptations for this ecology, they would not be inhabitating areas that are frequent sites of preservation of skeletal remains, like rivers or lakes. It is no coincidence that freshwater aquatic animals like various temnospondyls and crocodilians have a pretty good fossil record. Lastly, modern caecilians are predominantly found in the tropics. These regions, while home to some of the greatest biodiversity in terrestrial environments, are also not very conducive to fossilization because humid/moist environments promote rapid decomposition of remains. Add these up and you have a recipe for a depauperate fossil record.

With nearly a hundred specimens attributed to Funcusvermis (and many more that were subsequently picked out of the sediment after we had begun finalizing this paper), we've nearly doubled the entire fossil record of caecilians based on specimen number, all from just a single remarkable site in the middle of the Arizona desert. The below figures show the relative abundance of specimens and individuals of Funcusvermis to the rest of the caecilian fossil record.

This isn't a case of many elements of a few individuals as well. The site's (published) MNI is established at a whopping 76 individuals based on lower right jaw elements (pseudodentaries), increasing the number of distinct caecilian individuals represented in the fossil record by an even greater magnitude. For some reason, nearly all of the elements are from the right side of the body, a skew that wouldn't be expected using a thorough process like screenwashing in which there's careful sorting of both fragmentary and complete elements of all taxa (this is the one time that people don't throw the temnospondyls out). We're still figuring that part out...

Perhaps the best place to start with "where does Chinlestegophis stand now" is to discuss where Chinlestegophis stood before this. Acceptance of the hypothesis of lissamphibian origins has been tepid at best and practically non-existent at worse. Per Google Scholar, Pardo et al. (2017) has been cited 62 times. When you cut out unidentified duplicate entries, theses/dissertations, preprints, and conference abstracts, the number comes down to 50 (there are a few that it misses that ResearchGate catches). Somehow, I think I am the most frequent citer of this paper actually – 13 first-authored papers that do so. Nearly all of these citations, mine included and particularly those from paleontologists, are "neutral" – they profess no personal stance on the hypothesis of Pardo et al. and do not attempt to directly tackle the question. Some examples:

• "The origin of some or all lissamphibians is hypothesized to fall among small upper Carboniferous temnospondyls, the amphibamiform dissorophoids (Bolt, 1969;Anderson et al., 2008a;Maddin et al., 2012;Pardo et al., 2017;Schoch, 2019)." – Schoch et al. (2019)
• "Nonetheless, the origin of lissamphibians remains uncertain (Pardo et al., 2017; Marjanović and Laurin, 2019)." – Dilkes (2020)
• "Despite an increase in knowledge on the fossil record of lissamphibians (e.g. Gao & Shubin, 2003; Jenkins, Walsh & Carroll, 2007; Skutschas & Martin, 2011; Ascarrunz et al., 2016), their interrelationship as well as their origin (or origins) from the vast range of early tetrapods remains a matter of debate (Laurin & Reisz, 1997; Meyer & Zardoya, 2003; Schoch & Milner, 2004; Ruta, Coates & Quicke, 2003; Ruta & Coates, 2007; Sigurdsen & Green, 2011; Marjanović & Laurin, 2013; Schoch, 2014; Pardo, Small & Huttenlocker, 2017a; Pardo et al., 2017b)." – Danto et al. (2019)

Other studies have directly challenged the results and conclusions of Pardo et al.:

• Santos et al. (2020), which presents a summary of the fossil record of gymnophionomorphs, dedicated an entire section to arguing against this hypothesis.
• Marjanović & Laurin (2019), mostly in passing, alluded to the weakness of the original results, which reported only a majority-rule consensus, as the strict consensus does not support the novel hypothesis, and the typical monophyletic origin from within dissorophoids was among a smaller subset of most parsimonious trees.
• Serra Silva & Wilkinson (2020) dedicated an entire study to demonstrating how the use of a majority-rule consensus is flawed when inferring evolutionary relationships, with the single case study being the original dataset analyzed by Pardo et al.
• Both Schoch et al. (2020) and Daza et al. (2020) independently recovered the traditional temnospondyl hypothesis when using slightly modified and slightly expanded versions of Pardo et al.'s dataset, and I (via my preprint) have shown that correcting for systemic issues in the source matrix for Pardo et al. does not recover their novel topology upon reanalysis regardless of which consensus method is used (in general though, the rest of my citations of this paper would be considered "neutral"). David Marjanović also had an SVP talk last year (see p. 233 of the abstract volume) challenging Pardo et al.'s methods and hypothesis.
  

All of this is to say that, like Anderson et al.'s (2008) polphyly hypothesis, the diphyly/new polyphyly (depending on how you want to cut it) hypothesis is not exactly causing anyone to rewrite any textbooks, and it has not gained really even marginal acceptance among workers not affiliated with the study.

With that being said, I would summarize my opinion of Chinlestegophis, which hasn't really changed over the years, as an "interesting and plausible idea that fills some notable conceptual / data gaps but that is not well-supported quantitatively or phenetically." I won't beat the proverbial horse again on the phylogenetic bits, which are re-summarized briefly in our supplemental data, but I will spend some time going through the qualitative comparisons and arguments (but read the supplement, I wrote a lot more in there).

Most of my reservations have more to do with how Chinlestegophis is compared to other temnospondyls and caecilians, rather than the anatomical interpretation of Chinlestegophis (at least Schoch et al., 2020, dispute their identification of a lateral exposure of the palatine). I find many of the favorable comparisons made by Pardo et al. to either be oversimplifications or mischaracterizations. Let's take two examples of co-ossification that are proposed to be shared between Chinlestegophis and some other tetrapods:

• Purported to be shared with brachyopoid temnospondyls and caecilians: lacrimal coossified to maxilla
  • In Chinlestegophis, Pardo et al. (2017) identified the nasolacrimal duct passing through the top of the maxilla. In other temnospondyls, this typically passes through the lacrimal, but Chinlestegophis has no distinct lacrimal; on this basis, Pardo et al. inferred that these two bones had co-ossified. Whether this is actually shared with any other temnospondyl is debatable at best and total speculation at worst; there are a variety of non-brachyopoids that lack a lacrimal (e.g., tupilakosaurid dvinosaurs, some rhytidosteids, some trematosaurs), but it has never been demonstrated via the same nasolacrimal duct proxy, which requires either CT scanning or a really serendipitous break, that the lacrimal co-ossifies with anything in those taxa; complete loss is another option. There is no biological law that says if a distinct lacrimal is absent, it must have fused with the maxilla.
• Purported to be shared with stereospondyl temnospondyls and caecilians: opisthotics coossified to exoccipitals
  • The opisthotic is one of three bones considered to be part of the inner ear of early tetrapods; the other two are the prootic, a bone you are unlikely to ever see in full form without a CT scan, and the stapes, a rod-like bone responsible for conducting sound with whatever external ear system (e.g., a tympanic membrane) existed in these animals. The assertion by Pardo et al. that opisthotics coossified with the exoccipitals is a shared feature with stereospondyls is strange because the inner ear, and most of the braincase, is exceptionally poorly ossified in most stereospondyls on account of their paedomorphic nature. There  are many taxa in which the opisthotic is not ossified at all, and in nearly all others, it is either not co-ossified with the prootic or is not co-ossified with the exoccipital. When this does occur, again, rarely, it is only in exceptionally large stereospondyls like Mastodonsaurus, which is one of the largest known temnospondyls, and thus the co-ossification in those taxa is likely a result of large size. The more common condition, across temnospondyls and early tetrapods alike, is for the exoccipital to co-ossify with the prootic to form a joint otic but to remain separate from the exoccipital. The condition of Chinlestegophis in which the prootic is not mentioned as either a distinct or co-ossified element, is really weird in this respect and not like what we see in other temnospondyls.

I would encourage people who remain skeptical of our rebuttal of many of the original claims of Pardo et al. to read section 3 of our Supplemental Information; I spent a lot of time on that...

Today, caecilians occur within a narrow latitudinal belt (27° N and 34° S), and their fossil occurrences are bracketed between what would have been around 16° N and 27° S. This constrasts sharply with both the fossil and extant distribution of frogs and salamanders, the former of which make it nearly to the poles. Understanding the present distributions of different groups of tetrapods necessarily requires a look into the deep past to understand how the continents were arranged and how different organisms could or could not get around.

All lissamphibians are susceptible to drying out because of their wet skin and their use of it to breath (cutaneous respiration), but caecilians are particularly susceptible to dry environments, which is one reason they spend a lot of their time below ground where it's more humid/damp. Even though caecilians were already established at a time when the continents were largely still connected, allowing the dispersal of all sorts of different organisms around the world, that their fossil occurrences remain tied to this narrow equatorial belt indicates that early caecilians were also more climatically sensitive than other lissamphibians, and thus, that caecilians' present distribution has been strongly constrained by the presence or absence of humid environments. It's a strong reminder of the ways in which the past directly shapes what we observe in the present and underscores the importance of studying the deep time record of the planet and its inhabitants in order to really understand how we ended up with today's ecosystems.

It was a relatively quiet year on the temnospondyl research front – I think we may be seeing the real effects of the pandemic accumulating now, as people have started running out of leftover projects. By my count, there were just 17 papers either focusing entirely on temnospondyls or with a substantial temnospondyl component, and four of those were published just in the past two weeks! Nonetheless, there was some very exciting work this year, including a disproportionate amount of metoposaurid studies; this seems to be in a trend in recent years, driven almost entirely by teams working on the Polish material, which is a real testament to Krasiejów. I think there is some exciting stuff coming up the pipeline in 2023 (not from me), and I am looking forward to hopefully a more productive year for temnos!

Werneburg et al. (PalZ) described a new zatracheid, represented by an essentially complete skeleton, from the early Permian Chemnitz Fossil Lagerstätte in Germany, Chemnitzion richteri. This deposit records the dying moments of a terrestrial environment being buried in ashfall and the subsequent pyroclastic flow of a volcanic eruption, thus preserving a remarkable diversity of organisms (including plants and invertebrates) in 3D natural molds and casts. Despite a decent number of specimens, zatracheids remain relatively rare in the fossil record – both Acanthostomatops vorax (Germany) and Dascyeps bucklandi (England) are only known from a single site, which may reflect the lower frequency of dryland habitats recorded in the Permo-Carboniferous of Europe compared to North America. The postcranial record of the clade is also only known from Acanthostomatops, and the nearly complete skeleton of C. richteri provides further details on the variation within zatracheids.

Schoch & Sues (Journal of Paleontology) provided a long-awaited reassessment of the enigmatic early Permian temnospondyl Parioxys ferricolus. Despite being known from an appreciable sample size of specimens from Texas, the anatomy and taxonomy of this taxon have long been confusing because the original descriptions were limited to what are now grainy photographs and stylized reconstructions. The original descriptions from nearly 70 years ago were influenced by the  descriptor's (Y. Shawki Moustafa) hypothesis that Parioxys was closely related to Eryops in how comparisons and reconstructions were made, but other workers have long-suspected that the taxon might belong to a different clade. Schoch & Sues' redescription and reassessment provided more compelling evidence for dissorophid affinities, specifically with the cacopines, based on features like a transverse nuchal ridge on the postparietals, a foreshortened posterior skull table, and modified features of the palate.

Fresh off the press from last week is a revision of the Middle Triassic trematosaur Trematolestes hagdorni by Schoch & Mujal (Neues Jahrbuch für Geologie und Palaöntologie). When originally described in 2006 by Schoch, the taxon was represented by a number of essentially complete specimens, but these were interpreted as belonging to immature specimens. New material described in this study greatly expands the ontogenetic range on both sides, from highly immature individuals to demonstrably mature adults. The ontogeny of many trematosaurs (and arguably most stereospondyls) remains very poorly known due to a lack of variably sized specimens, and the new material of Trematolestes represents the most completely known ontogeny among Trematosauria.

Another hot off the press paper, Surmik et al. (BMC Ecology and Evolution) report the oldest unequivocal occurrence of osteosarcoma (bone tumor) in the vertebra of an "amphibian" (non-amniote). Given the scarcity of pathologies in the fossil record in general, it likely comes as little surprise that this osteosarcoma was identified from the extensive sample of Metoposaurus krasiejowensis from the Late Triassic Krasiejów locality in Poland. Through CT scanning and histology, the authors provided a detailed description of the tissue type and organization, which permitted their diagnosis.
   One of the interesting discussion points raised by the authors is the scarcity of identified occurrences of cancer in fossil "amphibians" given their sample size; indeed, I have never seen such a malformed intercentrum out of perhaps >1,000 that I have seen in North American collections. Modern amphibians have a relatively low rate of reported bone cancer (most occurrences of cancer are reported from the skin), and the authors speculated that temnospondyls may have been similarly resistant to cancer through a variety of developmental and genetic mechanisms.

One of the distinctive features of stereospondyls is their massively enlarged pectoral elements, which form large, plate-like structures. It has often been assumed that such bones would serve as ballast to help these animals sink to the bottom of water bodies; increasing bone weight and/or density is a common feature among many aquatic animals. However, general size is not necessarily reflective of weight (although in fossilized form, it certain does) – bone compactness is the real metric that can be used to assess how a bone contributes to buoyancy. Kalita et al. (Journal of Anatomy) compared the compactness of the clavicle and interclavicle of Cyclotosaurus intermedius and Metoposaurus krasiejowensis and found a high degree of compactness in both taxa. However, differences in microanatomical structure hint at different lifestyles (Metoposaurus more benthic, Cyclotosaurus more active swimming), corroborating other research suggesting interspecific niche partitioning. At least among the several sampled specimens of Metoposaurus, there was no indication of intraspecific niche partitioning, indicating a benthic lifestyle was adopted quite early. 

Weryński & Kędzierski (Geological Quarterly) used both histology and SEM to examine the external and internal microstructure of teeth of Metoposaurus krasiejowensis (yes, it's another year filled with research on Polish metoposaurids). In addition to the typical labyrinthodont infolding that has been known for over 150 years in temnospondyls, the authors also identified directional porosity in the canals making up this structure that they interpret as an adaptation for counterbalancing stress forces during biting. Additionally, they identified what they interpret as growth marks within the teeth, equivalent to four seasonal cycles, which adds to the data used to assess the perceived biological response to any local climatic periodicity.

Title: Revision of the Late Triassic metoposaurid “Metoposaurus” bakeri (Amphibia: Temnospondyli) from Texas, USA and a phylogenetic analysis of the Metoposauridae
​Authors: B.M. Gee; A.M. Kufner
Journal: PeerJ
DOI: 10.7717/peerj.14065

General summary: Frequent readers of this blog are of course familiar with my love for metoposaurids, one of the most iconic groups of North American temnospondyls. It is no secret that metoposaurids were my "gateway drug" to the world of terrifyingly large and unrecognizable amphibians, and so they always have a special place in my heart. My previous research has largely focused on two of the three species, Anaschisma browni (ex. Koskinonodon perfectus, ex. Buettneria perfecta) and Apachesaurus gregorii, which are the two most common metoposaurids that we get in the Late Triassic of North America. If you go to a museum and see a metoposaurid (most major museums in the U.S. have a metoposaurid on display), it's likely Anaschisma browni, although the label may be two or three junior synonyms out of date. The third species, known only from two sites in Texas and one site in Nova Scotia, doesn't get as much press - it was last (re)described in 1932! Ninety years later, my buddy Aaron Kufner and I are pleased to produce a full redescription of this taxon, long referred to as 'Metoposaurus' bakeri, based on a reexamination of material from the type locality that now lives at the University of Michigan Museum of Paleontology (UMMP) collections in Ann Arbor. With a thorough redescription spanning 134 print pages (probably too thorough, even by my own standards), we provide extensive documentation of the skeletal anatomy of this species (1930s-era drawings have their limitations), conducted more phylogenetics analyses to test the relationships of metoposaurids (this has gotten no better since the 1930s), and ultimately concluded that this species cannot be placed in an existing genus like Metoposaurus (otherwise only known from Europe). To that end, we created a new genus name, the mouthful Buettnererpeton, which honors a longtime fossil preparator at the UMMP, William H. Buettner, who worked extensively with E.C. Case, the museum curator who named the species in 1931. The suffix comes from -herpeton, meaning 'creeping animal' in Greek, which is a common component of names of early reptiles and amphibians. Our taxonomic act has implications for biostratigraphy (relating distantly situated rocks based on which taxa occur in them), both globally and within North America, and we discuss everything from future work needed on metoposaurids to why their phylogenetic relationships are so badly resolved. This is a 'boundary-crossing' project that originated when I was a Ph.D. student in the summer of 2019 and has only now made it to the finish line, so it is particularly memorable for me in that regard.

Most of the excessive taxonomic splitting (naming new species based on features that are not considered reliable for taxonomic differentiation, like size of the type specimens), has been historically concentrated in North America and Europe, but it's been fairly stable in North America for a few decades now, with everyone agreeing that there are three valid species. I've tackled two of these in recent years, Anaschisma browni (the one that keeps getting renamed, much to the chagrin of museum exhibit designers) and Apachesaurus gregorii, but the remaining metoposaurid is the least well-studied and thus the most taxonomically ambiguous: "Metoposaurus" bakeri (which you can find with pretty much every combination of genus + species, both with an without quotes, e.g., Koskinonodon bakeri, Buettneria bakeri).

The rationale for the updated taxonomy is entirely normal for paleontology but illustrates the subjectivity associated with how scientists differentiate at a given taxonomic scale. "Metoposaurus" bakeri was primarily allied with Metoposaurus diagnosticus because both taxa purportedly shared the condition of having a lacrimal bone that was separated from the orbit, in contrast to Anaschisma browni (then "Buettneria perfecta"), which has a lacrimal that enters the orbit (see above on right). That's it, one binary feature. "Metoposaurus" bakeri was then differentiated from M. diagnosticus by several qualitative features, like a proportionately longer lacrimal and a smaller area of radiating grooves on the clavicle. Both are (1) really continuous, not discrete, and (2) shared with A. browni. Other shared features have also been argued to separate the North American taxa from Metoposaurus proper from Europe, like the relative size of circular pitting on the interclavicle (see below). All of this is to say that an argument could have been made to unite "M." bakeri in the same genus with A. browni, and to use the lacrimal-orbit relationship as their one differentiating feature.

This convoluted history brings us to this study. Whether "Metoposaurus" bakeri really belongs in Metoposaurus or not has big implications for both metoposaurid taxonomy and biostratigraphy. If "M." bakeri was placed in Metoposaurus, this would further undermine the historical use of the lacrimal-orbit relationship as a differentiator of metoposaurids at the genus level. The reason why this is so problematic is not the undoing of precedent (a lot of historical precedent should be undone) but rather that the only reliable diagnostic cranial feature of Metoposaurus (in the sense of Brusatte et al., 2015, in which only the three European species belong to this genus) and Anaschisma is the lacrimal-orbit relationship. In other words, if "M." bakeri were placed in either genus, it would mean that a lacrimal entering the orbit would no longer be diagnostic of that given genus, and therein, that would mean that many isolated skulls from North America or Europe would essentially be unable to be referred to a particular genus, let alone to a species. This would, for many reasons, be very bad for all paleontologists, not just academics. (It also illustrates that perhaps Anaschisma should be synonymized with Metoposaurus, as it was in the 60s and 70s).

However, there are options beyond trying to squeeze "Metoposaurus" bakeri into one of these two existing genera. Although I tend to be more of a 'lumper' than a 'splitter' in casual academic parlance (I tend to prefer synonymizing taxa than to create new ones), there was really no other option given the difficulty that we already have with differentiating metoposaurid genera. Hence, Buettnererpeton was born! This admittedly very wordy name takes its inspiration from the now-defunct Buettneria, a name created in 1920 by E. C. Case to honor a longtime colleague and fossil preparator at the University of Michigan, William Buettner. Finding some way to restore Case's homage was something that the collections manager, Adam Rountrey, had suggested to us back when we first visited in 2019, and combining Buettner's name with -herpeton, a common suffix for Paleozoic tetrapods (meaning 'creeping thing' or some variation of that), was the obvious choice.

One of the prominent regional patterns in the distribution of metoposaurids within North America is that there are very few on the eastern half of the continent, owing in large part of the much more limited exposures of Late Triassic rocks. Essentially all of the ones on display are from Arizona, New Mexico, or Texas (even the ones housed in east coast museums like the Smithsonian, American Museum of Natural History, and the Museum of Comparative Zoology). Most metoposaurid material from the eastern seaboard was collected during the construction of tunnels, which as you might imagine, was less than conducive for the collection of delicate fossils. As a result, practically none of it is diagnostic to a certain species, and it requires a fair bit of circular logic to even assert metoposaurid identity at all.

The one exception to this is a very nice natural mold of Buettnererpeton bakeri from Nova Scotia, also one of the few nice Mesozoic temnospondyl fossils from Canada. This specimen was first collected several decades ago (and now lives at Yale) and has long been the only occurrence of B. bakeri from outside of Texas. Although its identity hasn't been particularly controversial, Hans kindly gave us a good photograph, from which we reproduced an interpretive line drawing (not previously done), to corroborate its conspecificity with the Texas material. Its isn't that surprising that metoposaurids would have lived there - they are found in Morocco and western Europe, which would have been much closer to the eastern seaboard in the Late Triassic - but it does demonstrate the geographic range of one species. Really broad geographic ranges are only something that we observe in North America, likely due to a combination of the large size of North America compared to Europe, the heterogenous geography of the Late Triassic, and the heterogenous distribution of Late Triassic exposures today. But it's nonetheless important for indicating that metoposaurids were likely distributed across much of North America and are only unknown from many parts because of lack of Late Triassic exposures. Quite possibly, they were as widely distributed as common living fauna like raccoons.

One of the longstanding practices in paleontology was naming new species when something was found in a new region. Of course, perceptions of geographic distance can be greatly exaggerated by the modern configuration, when in fact what are now disparate regions could have been closely situated in the geologic past. The general amalgamation of the continents into Pangea was largely consistent throughout the Triassic, as seen below.

As a result, most of the metoposaurid-bearing regions are actually quite close to each other. Nova Scotia was very close to the Argana Basin of Morocco, from which many metoposaurids have been collected, closer in fact than it was to the southwestern United States. At the time, Nova Scotia was about as close to Germany as it was (is) to Arizona. The below figure from Brusatte et al. (2015) illustrates this well, demonstrating that there was a strong latitudinal constraint on the distribution of metoposaurids, which have yet to turn up in the well-explored Late Triassic of South America.

"Metoposaurus" bakeri figured somewhat prominently in the attempts of some workers to make correlations in relative age between geographically disparate regions around the world. Dating back to the old framework of Hunt (1993) in which Metoposaurus was found in both North America (viz. "M." bakeri) and Germany (viz. M. diagnosticus), certain workers honed in on Metoposaurus as a possible index taxon, a species or genus that is sufficiently common and widespread to serve as one of the markers used to correlate rocks deposited in disparate regions. At the time, no other genus and no species was found on more than one continent; most are actually quite restricted. However, old-school taxonomy is often conceptually suspect, and as a result, a lot of these index taxa have been diminished in biostratigraphic value. Sometimes it's shown that the occurrence in one region is not actually that taxon, so there is no direct correlation. Other times, original identifications were somewhat circular in logic or based on very fragmentary material, leaving a lot of doubt. This is not exclusive to metoposaurids, which has led to a stark bifurcation in utilized taxonomic frameworks of all sorts of Triassic tetrapods, with proponents of an ability to use terrestrial tetrapods for global biostratigraphy preferring older (outdated) frameworks that maintain the utility of this global system. This is likely an unstated rationale behind certain workers preference to maintain "M." bakeri in Metoposaurus, even after studies demonstrating that they do not actually share the lacrimal excluded from the orbit.

Our formalization of a new genus for "M." bakeri puts the final nail in the coffin for the use of metoposaurids for global biostratigraphy (although I'm sure that proponents of this scheme will continue to push the old framework). With this, no metoposaurid genus or species is definitively found on more than one continent, and most are restricted to a single depositional basin. Although metoposaurids were clearly widely spread globally thanks to the formation of Pangea, it's not surprising that taxonomic divisions along some of the modern continental boundaries as the supercontinent started to break up. Metoposaurids have never been shown to have saltwater tolerance or to be particularly capable of much terrestrial locomotion (i.e. they were limited to dispersal in freshwater). Consequently, even a narrow separation induced by, say geography, could easily result in allopatric speciation along contemporary continental bounds, kind of like the famed Grand Canyon squirrel speciation example that is often cited in high school biology books. Of course, it is important to note that the time intervals preserved on each continent or within a given depositional basin are rarely the same, so we don't always have a precise apples-to-apples comparison, but as of right now, metoposaurids are no longer viable for global biostratigraphy.

Despite an impressive surge in metoposaurid work within the past decade (more than 20 papers focusing exclusively on metoposaurids, with many others including them in a broader sample), there remains a lot of work on all fronts for metoposaurids. We outline many of these in the paper, and I'll list a few of them below.

Phylogenetic grass
The phylogeny of metoposaurids remains utterly unresolved, which is not really that surprising when considering the limitations of morphology-based phylogenetic inference for any clade and the stark conservatism in metoposaurid morphology. Through a series of differnet analyses, we demonstrated that resolution is highly sensitive to minor differences in algorithms, analytical methods, and scoring philosophy such that it's quite hard to be confident in most nodes. Certainly I think that people could do more testing (there are a million different combinations of settings), after the first set of computer-assisted phylogenies from Chakravorti & Sengupta (2018); Buffa et al. (2019); and Gee et al. (2019), this one has pretty clearly demonstrated that we are going to need a lot more data (i.e. more fossils) to even have a chance of producing any topology with measurable support for recovered nodes.

Apples and oranges
One of the often unstated limitations to the metoposaurid record is that most taxa are only known from what are probably already adult individuals. We know nothing of whether there was a larval stage in metoposaurids or of what ontogeny looked like at skull lengths less than 10 cm (metoposaurids could reach at least 65 cm or so in skull length). One of the intriguing yet oft-overlooked aspects of this incomplete record, which we illustrate below, is that one of the lesser known metoposaurids, Arganasaurus lyazidi from Morocco, is only known from small specimens. This attribute is much better known and discussed for Apachesaurus gregorii, but although the describer of Ar. lyazidi, Jean-Michel Dutuit, speculated (in French) that it might be a dwarfed taxon, this has never been adopted by other workers, let alone tested. It's interesting to juxatpose this against the growing acceptance of my proposal that Apachesaurus is also not a dwarf taxon, although certain workers continue to advocate this while ignoring all of my previous studies (likely because they have no way to refute the histological data and related arguments). How the disparity in distribution of known specimens might in general affect our interpretations of metoposaurid taxonomy (are some purportedly diagnostic features really ontogenetic features) remains to be well-explored and arguably requires someone to get lucky and find some breeding pond or something of the sort.

Old horizons
One of the downsides of being an extremely common taxon is that people rarely collect your fossils. Metoposaurids are so abundant that there is an unspoken predisposition against spending a lot of time collecting metoposaurids, which are on the larger side of the Late Triassic tetrapod scale and definitely on the upper end of the most abundant group known from the Late Triassic of North America. One of the problems is that this leads to a lot of poorly documented reported occurrences, which get dodgier as you work down to a particular genus or species. Most reports of North American metoposaurids are asides in faunal lists or review papers, and they don't provide photographs, description, or even specimen numbers. As a result, a lot of these "reports" are not reproducible. Particularly in North America, this translates into irreproducible stratigraphic ranges - what are the highest and lowest occurrences of the given taxa. In some instances, there is good documentation of the fossils, and it's the sites that are just not well-constrained stratigraphically (this is the case for B. bakeri's three localities), but for Anaschisma browni and Apachesaurus gregorii, which have thousands of specimens referred to each of them, it's more often that the stratigraphy is reasonably well-resolved, and the taxonomy is suspect (or at least not demonstrated). The North American taxa are particularly susceptible to circular logic where both size and stratigraphic position are used as identifying features in the absence of any actually diagnostic anatomical features.

The outcome of this is extreme uncertainty in what are the actual stratigraphic ranges of these two taxa, indicated above by dashed lines. The debate over Apachesaurus and whether small, elongate intercentra are really diagnostic for the taxon or just a hallmark of early ontogeny in North American metoposaurids has a huge impact on both the total abundance of specimens and the stratigraphic range of this taxon. Therefore, establishing the true range of these taxa will require a huge undertaking that involves both revisiting of specimens thought to be near the upper and lower bounds to determine whether they are diagnostic and revisiting of the sites that they come from to determine whether they are actually where previous workers have situated them.

Title: Cold capitosaurs and polar plagiosaurs: new temnospondyl records from the upper Fremouw Formation (Middle Triassic) of Antarctica
​Authors: B.M. Gee; C.A. Sidor
Journal: ​Journal of Vertebrate Paleontology
DOI:  10.1080/02724634.2021.1998086

General summary: The Middle Triassic captures a diverse global record of temnospondyls, which is also when we start to see the pinnacle of the evolution of large body size, with many taxa routinely exceeding skull lengths of half a meter and body lengths of probably 2m or greater. A variety of different groups are present at this time, all of which appeared in the Early Triassic and which would also continue through the Late Triassic, and many ecosystems were host to several different species of no close relatedness. However, the Antarctic record of Middle Triassic temnospondyls has only comprised members of a single clade, the capitosaurs. Dated and brief historical notes suggested the possible presence of another clade, the long-snouted crocodilian-like trematosaurs, but this was never substantiated, and thus the Antarctic record, despite preserving at least three different species, captures an overall much lower diversity of temnospondyls than found elsewhere around the world. In this study, we took a look at some of this more ambiguous historical material, combined with more recently collected material of some very large lower jaws. While every single one of these lower jaws belongs to a capitosaur, there is a partial interclavicle (part of the shoulder girdle) that is very clearly not that of a capitosaur but instead that of a plagiosaurid, a peculiar short-snouted clade that has hundreds of records from the northern hemisphere but a mere two others from the southern hemisphere (both of those are from the Early Triassic). We speculate on some of the reasons why the Antarctic record, which is undoubtedly undersampled, might reflect real patterns of differing ecologies among large-bodied temnospondyls (i.e. 'big crocodile analogue' is a gross oversimplication).

Globally, the Middle Triassic record of temnospondyls is quite diverse, with extensive records of many of the large-bodied taxa that people often associate with the Mesozoic. This includes the short-snouted brachyopids and plagiosaurids and the long-snouted capitosaurs and trematosaurs. Often, we find localities with multiple species, if not multiple families, of different temnospondyls, indicating that they were flourishing during this time period. The Antarctic record is therefore interesting because to date, there are only capitosaurs! Previous records mostly include brief reports of fragmentary material (e.g., Hammer, 1990), but more recently, three different genera, two of them entirely new, have been documented by Chris and colleagues (Sidor et al., 2007, 2008, 2014; see below). Some of these newer fossils are traveling around the U.S. right now as part of the traveling Antarctic Dinosaurs exhibit (currently in Buffalo at the Buffalo Museum of Science).

We also looked at more recently collected material from approximately the same localities/horizons as the historical material. This material also only included lower jaws that appear to be capitosaur in nature. Some are also remarkably large - the scale bars below are 5 cm, and conservative estimates indicate that some of these lower jaws would have been more than 90 cm long, which ranks among the largest temnospondyl specimens known from the Triassic (most capitosaurs aren't known to exceed about 60 cm in skull length). So not only do we only have capitosaurs, we have only very mature individuals, which makes sense given that these remains come from a coarse sandstone that represents a high-energy setting that would have been less conducive to preserving the remains of juveniles.

This specimen isn't just notable for being the first plagiosaurid from Antarctica, but also for being the first plagiosaurid from anywhere in the southern hemisphere in the Middle Triassic. One of the ideas that we advance here is the notion that plagiosaurids were pioneer species, something previously postulated based on bone histology (e.g., Witzmann & Soler-Gijón, 2010; Sanchez & Schoch, 2013). In this scenario, plagiosaurids would have been well-adapted for more unstable environments that could have seen fluctuations in oxygen content, salinity, and other aspects of water chemistry, and these habitats may not have been so great for other temnospondyls. Conversely, plagiosaurids may thus not have been as common in more stable habitats that were frequented by other temnospondyls, like floodplains or high-energy rivers. There is some evidence for this in the temnospondyl-rich Late Triassic deposits of Germany, where plagiosaurids tend to be common in oxygen-poor environments where remains of other temnospondyls are rare but are rare in more stable environments where there is a greater diversity of other temnospondyls.

This still leaves the question of where are the trematosaurs? This clade is found throughout the world, including in the Arctic Circle, yet there is no trace of them in the Fremouw Formation, either the Early or the Middle Triassic exposures. One idea is that trematosaurs have often been cited as being euryhaline, as they are often (but not always) found in marine deposits. If so, it's possible that trematosaurs didn't inhabit the freshwater ecosystems in Antarctica (as they do in Germany, for example), and that the marine settings that they did inhabit around the south pole weren't preserved or haven't been discovered yet. If this were true, it would indicate that the Middle Triassic clades had settled into different niches, not only with respect to what they ate, but also what type of aquatic habitats they preferred.

Title: Returning to the roots: resolution, reproducibility, and robusticity in the phylogenetic inference of Dissorophidae (Amphibia: Temnospondyli)
​Authors: B.M. Gee
Journal: ​PeerJ
DOI:  10.7717/peerj.12423

General summary: Phylogenetics, the means of inferring relationships among organisms and one way of classifying them, is a timeless part of paleontology, in part because our datasets are much more limited than those for modern organisms in which genetic barcoding is both widely accessible and robustly informative. As a result, there is often a lot more uncertainty and disparity among different analyses, and people should generally be skeptical when someone says there is a strong consensus for a given group, no matter how well-known (paleo nerds will definitely recall the debate a few years back about what 'Dinosauria' constituted). Temnospondyls are generally not well-known, and this means that they are not as well-studied. This often has the effect of resulting in one or two people producing a lot of the work for a given group, which can lead to an overstated consensus when the same dataset keeps getting used. Dissorophids, the armoured dissorophoids, are a great example of this. There is a ton of work, but pretty much everyone uses the same phylogenetic matrix. As you might imagine, analyzing pretty much the same dataset a bunch of times should lead to pretty much the same result, which would not be particularly compelling as a "consensus," but, SPOILER, there is in fact no consensus among these nearly identical analyses! That's a huge issue. This study delves into why, both through a separate phylogenetic matrix and from closely scrutinizing the previous one. There is a ton of data packed into it, but the short and skinny are that (1) previous studies have been compromised by systemic errors from the original; and (2) there is a general lack of resolution / of well-supported nodes among dissorophids (i.e. we don't know a lot more than we do know). Then there's a bunch of other toss-ins like missing holotypes and chimeras. Keep reading to find out more!

This is an example of an admittedly "boring" paleontological study. There are very few pictures of fossils, none of which are particularly nice specimens; the results will never turn into some kind of remarkable paleoartistic reconstruction; and you will never hear about these findings in the news. Nonetheless, studies like this underpin the very foundations of paleontology and all of those attention-grabbing paleontology headlines, which hopefully will become apparent from this post / paper.

Before getting in to the details of this particular paper, I think it's important to give an overview of phylogenetics for readers who maybe don't know very much (or anything) about it. (Those familiar with phylogenetics can keep scrolling). I've touched on phylogenetics before in relation to some of my other papers, but I'll review some key terms and ideas here, beginning with "what is phylogenetics?"

• What is phylogenetics: Broadly speaking, phylogeneticists study the evolutionary relationships between organisms. This is a little different than systematics/taxonomy, which is how organisms are classified and categorized (e.g., in that old Domain-Kingdom-Phylum-Order-Class-Family-Genus-Species hierarchy you learn about in grade school). Phylogeny often informs taxonomy (this is cladistics), but it is not the only way to do taxonomy.
• How is phylogenetics done: In the pre-computer era, all phylogenetics was qualitative - scientists looked for what they thought were key features (e.g., limbs, feathers, teeth) and tried to find an evolutionary scheme that related organisms to each other based on whether or not they had these features. Certain features were more "generalized" (common), like teeth or limbs, while others were more "specialized" (rare), like opposable thumbs or wings. The shortcoming of this is that it's subjective - what features are considered or the relative weight attributed to them were up to the scientist. In the computer era, we have programs that have algorithms to quantitatively assess relationships. I go into more detail on this below!
• Why is phylogenetics important: Phylogenetics is often overlooked for two reasons: (1) it is very tedious and not really the kind of stuff people like reading about in NYTimes headlines; and (2) it requires a very in-depth knowledge of a certain group. However, phylogenetics underpins practically all biological studies because it relates organisms to each other. Any comparison therefore requires knowledge of how a given organism is related to another. For example, comparing animals with wings requires the context that many of them are entirely unrelated to each other - consider butterflies, birds, and bats as an example. Phylogenetics also provides the evolutionary narrative for how life has changed. Differences that seem very stark in the modern day make more sense when viewed through a deep-time lens of evolution and gradual changes and divergences.

The data. Data entry is the first step in computer-assisted phylogenetics. What we do is make a character matrix with a lot of numbers. The image below is a partial screenshot of one matrix that I worked with for this study. On the left-hand side, you have all the names of the different species being studied. On the top-row, oriented diagonally, you have names of different characters (these are different features being assessed). The rest is made up of numbers, which are colour-coded in this example.

Phylogeneticists begin by sampling taxa - which species do they want to study? Without going into details, paleontologists have particular challenges because some taxa are only represented by fragments, and these tend to be very bad for phylogenetic analyses because they are scored for very few characters, so usually these are omitted. It is very rare to include every species of a group that you are interested in. Then they sample characters - which features differentiate these species? A simple example:

• Limbs: present or absent.

Here we have a binary character related to the presence or absence of limbs. This is quite straightforward, but most analyses have characters that require in-depth anatomical knowledge of a group, such as "palatine partially or fully excluded from interpterygoid vacuity or not excluded at all." The different possibilities (e.g., present vs. absent) are called character states, and they are assigned numbers. An example:

• Limbs: present (0) or absent (1).

These are the numbers you see above. The majority of characters are binary - oversplitting can make things overly complicated. But you will sometimes see these multistate characters. An example:

• Tooth count: >50 teeth (0), 40-50 teeth (1), <40 teeth (2).

Data can be entered in other forms too. Molecular biologists use genetic sequences with base pairs (A, C, T, G, U) in place of numbers. But paleontologists only have morphological data, so we're left with these numerical schemes. Question marks, as you might imagine, represent missing data - the fossil record is not good enough to score that character for that taxon.

It's important to note that the simplest explanation is not always the right one. Life finds ways to do some really weird stuff. The gist is that parsimony is a workable baseline. Once we allow for more complicated solutions, the number of possible solutions increases exponentially, and it becomes both computationally expensive to search for them and difficult to actually figure out which one is the most likely (but this is where likelihood methods come in, which I'm not talking about here).

The output. A parsimony analyses will return what are called the most parsimonious trees (MPTs). There can be as few as one but are often many more. All of these MPTs have the same "length," which is given as a number of steps, which are essentially the number of evolutionary changes that had to occur to produce a tree with these relationships. If there are multiple MPTs, they will differ from each other at least slightly. In the example below, we recovered three MPTs. The red "taxa" (A–D) are ones whose relationships differ between each MPT. Note that some taxa may have the same relationships across all of the MPTs.

We then have different ways of summarizing the results (some of these are controversial).

• The strict consensus will "collapse" any node that isn't found in every MPT. For example, the relationship of A + B is found in the first and the third MPTs, but not the second MPT. That node is collapsed. The relationship of (A + B) + C is found in the first and the second MPTs, but not the third MPT. That node is also collapsed. A + C and (A + B) + D are each found in only one of the MPTs, so those nodes are also collapsed. Conversely, E + F is found in all MPTs, so it stays. This consensus is overly conservative. We do not believe that A, B, C, and D all split from each other simultaneously in an evolutionary sense. But because each MPT represents an equally parsimonious solution, we cannot discern in a quantitative sense which one is more likely.
• The majority-rule consensus will only collapse a node that is found in less than 50% of the MPTs (in this case, any node found in only one MPT). So while A + B is not shown in the strict consensus because it was only found in two of the three MPTs, it is shown in the majority-rule consensus. Now one of the reasons why people don't like the majority-rule consensus is because it can be somewhat misleading. For one, if you have hundreds to thousands of MPTs, the resultant majority-rule consensus might depict a tree that is not found in any MPT. In the simple example here, the majority-rule consensus is the same as MPT #1, but that doesn't always happen. Visually it can be misleading too. For example, you might be inclined to interpret the majority-rule consensus below as saying that A + B is found in 67% of MPTs and that (A + B) + C is also found in 67% of MPTs. The former is true, but the latter is not. (A + B) + C is only found in one MPT. (A + C) + B is found in one other MPT. So it is only accurate to say that A + B + C is found in 67% of MPTs.
  

There are other types of consensus methods (e.g., Adams, semi-strict) that I won't go over here, but you can read more about them in a pretty easy read by dinosaur paleontologist Tom Holtz here.

Okay, we are finally to the part where I talk about the actual study! This study looked at a group of dissorophoid temnospondyls, a group mostly found in the late Carboniferous and early Permian that I worked on for my dissertation (this is not part of my dissertation though). More specifically, I was looking at the large terrestrial dissorophoids, collectively known as olsoniforms (named after E.C. Olson) and which includes two groups, dissorophids and trematopids (yes, 'dissorophid' is one letter away from 'dissorophoid' and requires careful reading to avoid confusing).

Now what I wanted to do was to take the matrix I made for that 2020 trematopid study and expand it to include dissorophids, thereby forming an olsoniform phylogenetic matrix that comprehensively sampled all appreciably known taxa (no previous study has done this). What I ended up doing was a lot more than that, which is where the alliterative title comes in: "Returning to the roots: resolution, reproducibility, and robusticity in the phylogenetic inference of Dissorophidae (Amphibia: Temnospondyli)." I'll go through these three themes: resolution, reproducibility, and robusticity next.

Recent dissorophid phylogenies, shown below, display a range of resolution. There are two points of emphasis here. One is that disparity between studies. Most of these show large polytomies, but Liu (2018) nearly got the fully resolved tree that we're looking for. The second point speaks to what I commented on above - fiddling with the analysis to get resolution where none existed before. If you look at Dilkes (2020), there are two trees. The one on the left is poorly resolved. This is not very helpful for discussing relationships or evolution. The tree on the right is very resolved. We like that one! But to get that tree, Dilkes had to remove four taxa from the analysis. These taxa, often called "wildcards," are problematic in the sense that they confound resolution, whether because they are really fragmentary and have a lot of missing data or present weird combinations of features that don't line up with general trends. Removing wildcards is a common strategy to boost resolution, but like I said above, it inherently omits data that you know exist.

The problem crops up when people use the reduced-data results, which gives the more resolved tree, to talk about evolution and classification schemes, but then place omitted taxa in that framework. For example, Brevidorsum profundum is a typical dissorophid "wildcard." It's only known from one partial skull described in 1964 and is not well-preserved. Some people don't even think it's a dissorophid. Brevidorsum is either recovered within a large polytomy (uninformative) or is excluded from the analysis, but some workers constantly refer to it as being a member of a specific subfamily within dissorophids: Cacopinae (the dark green boxes). However, no recent analysis has ever demonstrated support for that, and this is where the old-school qualitative methods ("it sort of looks like that") and the modern quantitative methods ("the analysis says X") combine in a bad way.

My own analyses tended to recover very poor resolution. Sometimes this could be attributed to including a lot of pretty fragmentary taxa that aren't normally included (like the analysis shown above on left). When it looks like a giant comb...that's an uninformative tree. I could further extend that by showing that removing just a few taxa, some of which are not that badly preserved, could lead to a drastic increase in resolution (like the analysis shown above on right), similar to that example I just cited above.

Reproducibility is one of the foundational tenets of science. If someone does an experiment again, can they get the same results? The first step in this process is that it has to be clear how to reproduce an experiment. If you run a complicated study of colour preference in spiders, but only say "we picked some spiders and not others for this experiment" in your methods, it will be impossible for someone to know the specifics of how you did the experiment. So even if someone redoes an experiment on colour preference in spiders, it will likely not be the same as your experiment. Maybe they picked the wrong spiders. Or used different colour palettes. Etc. Because of this, whether their results are the same or not ("spiders like flaming hot pink") as yours, comparing them is difficult because differences in the methods could be responsible for the outcome.

In phylogenetics, the main areas where reproducibility comes into play are (1) the character matrix; and (2) the parameters of the analysis. Most journals require people to include their character matrix in one form or another, but ambiguity in the requirements is one problem – some people include their matrices in very inaccessible formats that have to be modified or typeset before a program can analyze them (even though the software to make universally accessible formatted files is F-R-E-E and easily available). In the simplest format, all of those scores in the nice GUI display as text strings:

• Example taxon A: 0000100002???0000???0

But often times people provide their scores in unhelpful fashions like this:

• Example taxon A: 00001 00002 ???00 00??? 0 [block format]
• Example taxon A: 0 0 0 0 1 0 0 0 0 2 ? ? ? 0 0 0 0 ? ? ? 0 [space-delimited]
• Example taxon A: 0   0   0   0   1   0   0   0   0   2   ?   ?   ?   0   0   0   0   ?   ?   ?   0 [tab-delimited]

Now these formats might help you read the string when the numbers are spaced apart...or you could just use Mesquite and have them all in a nice readable interface where you can colour code different character states and see exactly which character a score is for instead of having to count everytime, as seen below.

So when people don't provide their scores in an accessible format like the NEXUS file above, that means the next person has to edit or transcribe the data, which can introduce errors (indeed, I found a few errors in older studies where they had to transcribe it from a previous study and introduced a typo). Below is an example of a very inaccessible data matrix (the dissorophid matrix of Schoch, 2012); this is a figure of a table that cannot be OCR'd (even with the original publisher's version). This means that anyone who wanted to use this matrix would have to type out all of these scores themselves! That is a big waste of time.

Reproducibility doesn't always have to be about repeating the exact same experiment though – more straightforward experiments or ones where the results are intuitive (i.e. doesn't seem like there was data manipulation or accidental error) can be a waste of time to repeat except in coursework. So an alternative way to test reproducibility is to see whether an independent approach to the same question can recover the same solution. If the same general results are recovered, this really strengthens the argument derived from them. If there are different results, that provides an opportunity for future work to figure out why there are discrepancies.

One characteristic of most previous dissorophid studies is that they all draw from the same source matrix (Schoch, 2012; this is the blue bubble in the 2012 row in the figure above). This is common practice in science – taking an existing matrix and adding taxa of interest. It saves a lot of time because creating a new matrix is a lot of work! But there are two important points here. The first is that if everyone uses the same matrix and doesn't make many changes, each derivate of that matrix is not fully independent (we call these pseudoreplicates). Each pseudoreplicate is predisposed to producing the same results as the last iteration because the underlying data are nearly the same. So getting the same general result from five pseudoreplicates is not as much of a "consensus" as getting the same general result from five independent matrices. Essentially, this can be misleading and make you think that the results are very reproducible when that is really just because the data are nearly identical. This leads to the second point, which is that  the data must be solid when they're getting propagated, otherwise you're just propagating errors.

Immediately, there is a big red flag when looking at dissorophid phylogeny:

There is no consensus among these pseudoreplicates, in spite of being 99% similar to each other!. Not getting a consensus from a bunch of pseudoreplicates is really concerning because it indicates that relationships are not well-supported and can easily change with just the addition of one taxon or a few scoring changes!

The explanations. There are a lot of different explanators for why there are different results. Some of these are a little more towards personal preference in setting different parameters in the analysis. One probable explanation is that the taxon sample differs slightly between studies; those with more resolution tend to have omitted more of those "wildcards" that are weird or highly fragmentary. If you compare the results of Maddin et al. (part C above) and Schoch & Sues (part D above), this is a likely explanator for why the former is much less resolved - it includes historical wildcards like Brevidorsum profundum, fragmentary taxa like Broiliellus olsoni, and somewhat odd taxa like Reiszerpeton renascentis (the holotype of which was long considered to be an amphibamiform dissorophoid).

Taxon samples are low-hanging fruit for explaining topological differences. So I went deeper and started looking at specific cells in the matrix to see if there were perhaps typographic errors (I did find some of those). However, I found a lot more errors that do not seem to be typographic. I looked at the latest version of the Schoch (2012) matrix, which was the one published by Dilkes (2020). I identified over 140 scoring errors, which is a lot in a fossil matrix that only has up to 77 characters and 29 taxa. Many of these were instances where Taxon X was scored for Feature Y...except Feature Y isn't even known in Taxon X! One example is Cacops woehri from the Richards Spur locality. This taxon is only known from partial skulls, but somehow it was scored for a bunch of postcranial characters. Suspiciously, all 14 scores of this taxon that were erroneous were scored the same as Cacops morrisi, also from Richards Spur but which is fairly distinct from C. woehri. In fact, this deep dive revealed that the three species of Cacops, which are readily differentiated from each other, didn't actually differ in any scores other than their distribution of missing data (i.e. when they could be scored, they were all scored the same). This explains why all previous analyses recovered them as a single polytomy, when qualitative comparisons clearly show that C. morrisi and C. aspidephorus are much more similar to each other than to C. woehri (which might not even be Cacops).

Cacops was the most egregious example of what seems to be previous workers "assuming" scores that are not validated by the present fossil record, but other taxa also seemed to have scores here and there where a score was "assumed" based on the general affinity of that taxon (e.g., that some dissorophids with no known quadrate had a dorsal quadrate process preserved; this is a common feature in dissorophoids). This is, of course, a major problem! If you have what you think is a new species of Cacops, and you score it for a bunch of features of other species of Cacops,  you have pretty much guaranteed yourself of the outcome that you are allegedly testing because you have made this new species more similar to its alleged relatives than the fossil record actually bears out. Cacops aspidephorus is the best example of this - for over a century, nobody knew what the sutures were because the specimens were so poorly preserved. You could see this if you looked at reconstructions of the skull of different dissorophids, like from Schoch (2012) below. As you can see, C. aspidephorus is just a grey blob - no sutures. Why then, were there 15 scores for C. aspidephorus for characters that require sutures to be known? The sutures of the skull, based on a few specimens that were not so bad off, would not be published for another eight years until Anderson et al. (2020). In fact, other than characters with missing data for one or two of the three species, there were no characters for which one species of Cacops was scored differently than another.

Other issues relate to how characters are defined. For example, if a character requires skull length to be known, it doesn't make sense to score a taxon only known from specimens that aren't complete longitudinally. However, taxa like these were scored for these characters. Issues with characters like these that explicitly require certain landmarks but that seem to be scored in the absence of at least one were fairly common as well. In the examples below, both Brevidorsum profundum (only one specimen; Carroll, 1964) and Reiszerpeton renascentis (only one specimen; Maddin et al., 2013) are known from incomplete specimens. Therefore, their skull length is not actually known, but characters that require a ratio invoking the skull length were scored for these taxa previously.

As one might expect, correcting a large number of errors and then rerunning an analysis leads to drastically different results. On the left of the figure below are the original results from the Dilkes' matrix, and on the right are the results when the corrected version of the matrix is analyzed. There is a major loss of resolution! This suggests that at least some of the inconsistencies between previous pseudoreplicates of this matrix result entirely from erroneous scores in the matrix.

Furthering the issue is that these systemic errors didn't just appear in the latest version of Schoch (2012), published by Dilkes (2020). In fact, none of them were introduced by Dilkes, which I feel is very important to state, lest the reader think that Dr. Dilkes produces error-riddled work. Most of the errors go back to the original matrix and were thus introduced by Schoch, although some were separately introduced as taxa were added (e.g., Holmes et al., 2013; Liu, 2018). This means that every single previous study that used this matrix has also been compromised. I suspect, though I didn't test this, that correcting the same scores in all of the previous matrices would result in a loss of resolution in all of them, but this would actually boost the similarity between studies because the resolution of wildcard nodes would be eliminated.

One of the challenges with strictly morphological data is that there are just not very many datapoints. Compared to thousands to millions of genetic base pairs in molecular analyses, the average fossil tetrapod matrix has between 50 and 350 characters. This means that just a few scores could be responsible for a certain recovered relationship, whether a longstanding one or an entirely new one. Sometimes, even changing just a single score can change the entire tree! This is where support metrics come in.  These are statistical means of assessing how "strong" or "robust" a given node is; in other words, is this relationship likely supported by only a single score, and thus not very reliable, or are there many lines of evidence (scores) supporting it? In parsimony analyses, there are two conventional methods of assessing support.

Bootstrapping: Say you have a character matrix with 8 taxa and 14 characters. Bootstrapping is called "resampling with replacement." In one bootstrap replicate, the program will randomly select a character and its correspondent scores. Let's say it selects character #7 from the original matrix. This now becomes the new character #1 in the bootstrap. The program then picks the new #2 and the new #3 and so on. The caveat is that it can pick a character from the original matrix that was already selected. So it could pick character #7 three times in a row. It keeps picking until it has the same number of characters as the original matrix. Invariably, it is almost a given that some characters will be resampled multiple times, which means others are not sampled at all. Then you run this a lot of times (like 10,000) and calculate the percentage of these resampling replicates that nodes are found in. If you get low bootstrap support, that means very few replicates recovered that relationship and suggests that it is not well-supported because it is probably linked to one character. Bootstrap support over 50% (a node occurs in >50% of the bootstrap replicates) is considered "strong."

1. There is an alternative to bootstrapping, called jackknifing, which is "resampling without replacement." In this scenario, you designate a certain percent of characters to keep, and the resampling will keep that percent. So if you do a 60% cut, it will pick 60% of the characters (no duplicates like can occur in bootstrapping) and rerun the analysis, then repeat X number of times. This is rarely used in phylogenetics today, but the principle of jackknifing, termed "leave-one-out," is still common in other studies where analyses are repeated with a different data point omitted each time. This can help demonstrate the impact of outliers, for example.
   

Bremer decay index: Bremer support is an entirely different measure that has nothing to do with resampling. Bremer decay calculates how many additional "steps" are needed for a given node to collapse. This is exclusive to parsimony analyses as a result since it is predicated on the number of steps in the most parsimonious tree(s). Some programs have an automated way of calculating Bremer support, but the common way to do it is to get the MPTs and the number of steps among them, then get the strict consensus. Then you rerun the search and tell it to save not only the MPTs but also all trees that are +1 step longer. This will inherently be more trees and it includes trees that are not the most parsimonious. Then you get the results, compute the strict consensus, and if a node previously found is no longer found, that node has "collapsed." If it collapses at +1 steps, then its Bremer decay index is 1. You then proceed to do this search for all trees +2 steps longer, +3 steps longer, etc. >3 is considered "strong."

It is standard for scientists to report at least one if not both of these support metrics because it tells you how robust your recovered tree is. If a tree is not well-supported, then even one scoring error or dubious score could be producing this topology. Analyses with my matrix tended to recover low support for at least one of these metrics. I used a visual key to indicate whether a node was strongly supported or not by marking "weak" support in greyed-out text. You can see in the example below, which was an analysis of my matrix with the same taxon sample as Dilkes (2020), that there is a lot of grey... In fact, in this particular analysis, the only node with both strong Bremer and bootstrap support is the node for trematopids (orange circle), which was not even a focus of this analysis!

Previous dissorophid studies are a giant mixed bag. Some studies only reported one metric, and others didn't report anything. The latter is particularly bad because it emphasizes getting resolution (intentionally or not), no matter how weakly it might be supported or how few characters it might hinge on. This can lead people to "tinker" with the matrix, leaning one way when they're on the fence or specifically making modifications to certain characters or taxa until the expected or desired result comes out. It might be a reason why there were so many errors in the Schoch (2012) matrix in which one species was scored the same as another species in the same genus – scoring based on assumptions like this is a great way to boost both resolution and support. It's a reminder that even an "objective" quantitative method like computer-assisted phylogenetics is still underlain by subjective human decisions. Furthermore, when support is reported, it's often weak except for really large clades. For example, it isn't really that surprising or informative in a dissorophid-focused study that Dissorophidae is a strongly supported node unless you were suspicious about whether all dissorophids actually formed a clade (this isn't particularly controversial).

This is an example from the Dilkes (2020) analysis. As a reminder, "strong" support is Bremer > 3 (the first value) and bootstrap > 50 (the second value). Values near the bottom (more inclusive clades) are high, but they get really low as we go up the tree. Like my own analyses, trematopids (node E) have excellent support...but we're not studying trematopids in this analysis... Once you get into Dissorophidae (node J), which is what we wanted to study, no in-group node has Bremer > 1 (literally the lowest it can be) and most of them have bootstrap hovering around that 50% threshold. This isn't an indictment of the scientist, just to be really clear. But it does underscore that the topology of the tree is not the only thing that matters! Weakly supported relationships are just that – weakly supported.

Having already gone way further into the weeds than I intended to for this project, a lot of the discussion is a comprehensive synthesis of where things stand with dissorophids in their entirety. I overview Cacops, which could get a little help from a revision of Parioxys, a taxon originally interpreted as an eryopoid (and thus commonly placed as one in supertrees) but that in fact seems to share many similarities with Cacops. It has not usually been compared with dissorophoids at all, but could it be one? I also commented on Broiliellus, which is a dumpster fire of a genus. Nobody has ever recovered Broiliellus as a clade except by...you guessed it...excluding taxa. My preference is to restrict Broiliellus to the type species, B. texensis, and put everything else in single quotes (e.g., 'B.' reiszi) until this can be sorted out (some of these taxa have not been described since the 60s).

Then we have two more exciting discussions, the first a missing holotype and the second a possible chimera.

Allegedly, AMNH FARB 4785 should not exist! Dating back to the 60's, people said this specimen was missing. But I found it! (technically I found it in 2017 and said as much in a 2018 paper). But then where is AMNH FARB 4785a, which was apparently confused for AMNH FARB 4785? Concerningly, that specimen is nowhere to be found, and there is no record of it in the museum database or in their most recent inventory. It is always bad when a specimen goes missing, let alone a holotype. However, as far as I know, this specimen has never even been figured, only described generically as spines. It certainly wouldn't be the first time that a specimen just disappeared.

Above is AMNH FARB 11544. These are characteristic spines of Platyhystrix rugosa (part A). Coincidentally, this specimen was collected in 1881, the same year that AMNH FARB 4785a was collected, and they were both collected by the same guy from the same bonebed in New Mexico. However, AMNH FARB 11544 was not described or figured for a century until Berman et al. (1981). However, it meets the original description of AMNH FARB 4785 ("several spines") by E.C. Case in 1910, includes several that are in line with the measurements given by Case, and even includes a partial synapsid scapulocoracoid that was also mentioned by Case. The coincidence is almost too compelling! But there is no record of a number transfer, even after I checked with the AMNH collections staff (who have no record of AMNH FARB 4785a in their database on in the most recent inventory), so at present, the holotype of P. rugosa remains the missing AMNH FARB 4785a. I put this in the paper in the hopes that someone will be able to shed more insight on this...

Most examples of chimeras in paleontology are unintentional. They frequently result from assumptions that a collection of bones from the same spot, without excessive elements (e.g., five femora), belong to not only the same species but to the same individual. This is where preconceived biases can come in; everyone will have a list of "likely candidates" for a fossil when they come across it (e.g., you do not expect to find any temnospondyls in the Cretaceous Hell Creek Formation alongside Triceratops), but sometimes this list is too restrictive. A recent example is Dakotaraptor, a putative dromaeosaurid dinosaur (Velociraptor group) in which the purported wishbone turned out to be part of a turtle (see here). Another was a relatively rare report of a pterosaur pelvis from Canada that turned out to be part of a tyrannosaurid skull (see here and here). As far as I know, nobody's ever definitively identified a temnospondyl chimera.

That's where Aspidosaur binasser comes in. This taxon is based on one specimen from the Permian of Texas. It includes several skull fragments that collectively fill out most of the top of the skull and about 20 vertebral positions. This species is interesting for a couple of reasons. The first is that Aspidosaurus (like "Aspidosaurus" apicalis above) is a wastebasket taxon, encompassing a bunch of generally similar morphotypes that probably don't represent a single taxon. These morphotypes are largely isolated osteoderms that form an inverted V shape; cranial material of Aspidosaurus is practically unknown, which wasn't helped by the destruction of all material of the type species (which did include a skull), A. chiton, during an Allied bombing of Germany in WWII. So A. binasser is the best (and only) skull material we have. Then, A. binasser was described as having three different osteoderm types (shown below; figure from Berman & Lucas, 2003), which is unprecedented variation – other dissorophids only have one type, though it may change slightly in width or other minor attributes. And this is really where things start to get a little suspicious.

Despite having a good portion of the skull, including the occiput, which is the neck joint, and 20 vertebral positions from specifically the presacral (anterior to the pelvis) region, there is no articulation between anything. All three osteoderm types are found on their own; there is no block or fragment with two or three different osteoderm morphotypes on it. Then there is the peculiar question of where are the atlas and axis (the neck vertebrae)? Most dissorophids seem to have between 20 and 25 presacral vertebrae, so what are the odds of getting half the skull and 20 presacral vertebrae but not the neck vertebrae? If this holotype is a chimera, it would be really hard to prove because it's not like some composite Chinese bird that was Frankenstein'd together from different slabs, and all of the material does appear to be genuinely dissorophid in nature. And unlike how finding previously unidentified fits can positively prove association, not finding fits is not necessarily evidence for chimerism.

The original argument (more like assumption) for associating all of this material to a single species, let alone to a single individual, was that there was "no evidence for more than one dissorophid." This is, of course, negative evidence. Just because you don't find five femora doesn't mean that the two that you did find belonged to the same animal or species. Positive evidence would be definitive articulation. At the time, the recognized dissorophid diversity was much lower than it is now – we've had at least five new species named since then – and the interpretation that dissorophid-bearing sites only preserved one dissorophid species seemed to hold up (like with the Cacops Bone Bed). Since then, numerous examples of sites with multiple dissorophids have emerged. Especially at Richards Spur, we know that not only are there many species, but they are not equally abundant or represented by the same elements (more on this). So finding a cornucopia of dissorophid elements does not mean they all belong to one species or to one individual. Aspidosaurus is already known to be known almost only from isolated osteoderms (the same is true of Platyhystrix), so it is not unreasonable to argue that you could have some stereotypical Aspidosaurus osteoderms, possibly with an Aspidosaurus skull, mixed with random bits of other dissorophids.

So it is my suspicion that Aspidosaurus binasser is a chimera, but given the nature of its preservation, it is basically impossible to prove. Even if you found a specimen with the same skull that was articulated with vertebrae that only had one osteoderm morphotype, someone could (and probably would) argue that it's just a different species. This is a great example of the burden of dodgy taxonomy – it is very hard to undo (inertia), no matter how weak the original working assumptions were / are. At present, this is not a huge issue for phylogeny because there is no character for number of osteoderm morphotypes, but it is an issue for taxonomy because A. binasser and the functionally lost A. chiton are only differentiated on this feature.

Those who keep up with enough of my research know that one of my big themes is ontogeny, how we identify how mature temnospondyl specimens were at the time of death, and what not accounting for biases or skews in the fossil record might totally screw up our interpretations and analyses. I didn't focus on this too much with dissorophids as I did previously with trematopids, but there is a major disparity in size, which might correlate with disparity in the maturity of preserved specimens. Part of my thesis looked at Cacops and suggested, based on braincase morphology, that pretty much all known specimens of Cacops are juveniles at best, which underscores the point that just because you have a lot of the same size doesn't mean that was the largest size. This is definitely an interesting future direction though because cacopines like Cacops include the largest dissorophoids, which seem to get especially large in the middle Permian after lots of other Paleozoic temnos go extinct (including trematopids). Dissorophids are really diverse, and unlike trematopids, seem to have coexisted with other dissorophid species fairly commonly, so there could be legitimate major size differences between taxa that would lead to niche partitioning (e.g., one targets small tetrapods, one targets medium tetrapods, etc.).

This has been a longggg post. Hopefully it made sense if you read it all the way through, and if you did, thanks for reading! Hopefully you learned something new! This paper can really be distilled to four main points, which I also summarized at the end of the paper in a very atypical fashion for me just because of how much is packed in here.

1. There are systemic and widespread errors in the most widely propagated dissorophid matrix (Schoch, 2012). These are irreproducible and related to issues such as assumed scoring based on assumed close relatedness, which inherently compromises a phylogenetic analysis that is supposed to be testing hypotheses of relatedness.
2. People are not reporting support metrics enough, but they should be because this is equally important to the actual tree topology. A fully resolved but weakly supported tree topology is no good, and it should not be used to weave some elaborate story of evolutionary history.
3. You can get good resolution and decent support by cutting out taxa. This is not ideal because it is intentionally removing data that actually exist.
4. There is no consensus of relationships within dissorophids, within trematopids, or even within olsoniforms. People should not be using these really resolved trees when they need a phylogenetic topology as a backbone for other studies because they could contain spurious relationships and do not reflect a defensible state of dissorophoid study.
   

So coming back to why does anyone care. Phylogenetics relates organisms. If you don't know how things are related, it's harder to know whether their anatomy is remarkable or mundane, either in a qualitative or a quantitative sense. The flashy "big data" studies that examine really broad taxonomic swaths and big questions often use phylogenetic results because they need to – evolution guides patterns of morphology, behaviour, biogeography, etc. This puts a premium on getting good phylogenies because a bad one could lead you astray. This is why this kind of work, as well as descriptive anatomy, etc. remains really important to paleontology, even if it's considered "basic science." Without that foundation, nothing downstream makes sense (or it can be misleading or just straight-up wrong)! Especially with paleontology in which few things can be "known," constantly testing and improving these foundational datasets (which many find boring to do and some openly deride) is crucial for allowing us to reliably ask the broadest questions that we're all interested in.