The squamate tree of life from Simoes and Pyron 2021

From the abstract:
“With an evolutionary history dating back at least to the Middle Triassic at 242 Ma, the squamate Tree of Life also features numerous diverse but extinct branches, with hundreds of fossil species found all over the world.”

Firsts let’s look at clade definitions
According to Estes et al. 1988, Squamata is composed of Iguania + Scleroglossa. That is confirmed by the large reptile tree (LRT, 1845 taxa; subset Fig. 1).

If instead we made the mistake of following the more recent definition of de Queiroz and Gauthier 2020, “The largest crown clade containing Lacerta but not Sphenodon (originally Hatteria)”, then all members of the Iguania and two clade from Scleroglossa would be cut out of the Squamata, according to the LRT (subset Fig. 1).

Protosquamata: Lizard-like Lacertulus, Staurosternon and Palaeogama are all from the Late Permian. These are the last common ancestors of the Protosquamata, the proximal outgroup for the Squamata, which is a clade defined by extant taxa. All members of the Protosquamata (sans Squamata) are extinct.

From the Simoes and Pyron abstract:
“Despite their biological relevance both today and in the geological past, there remains a centuries-old controversy on how the major lineages of squamates are related to each other, with a direct impact on studies in ecology, evolution, paleontology, toxinology, and other fields.”

The LRT solved this controversy a few years ago by adding outgroup and ingroup taxa.

From the Simoes and Pyron abstract:
“Here, we provide a historical overview of this long research tradition, from 19th century naturalists to 21st century phylogenomics, with special emphasis on several recent advances over the last two decades. These insights have had a dramatic effect on our understanding of the squamate Tree of Life and clarify several possible future research agendas.”

Someone else needs to duplicate the methods and materials of the LRT to confirm or refute it. A historical overview may be interesting, but the leading edge is why we like science.

From the abstract:
“We provide an integrative perspective derived from genomics, morphology, and the fossil record and propose several points of synthesis in our current knowledge of broadscale squamate evolution and systematics.”

Genomics must be ignored. Too often that method recovers false positives.

“Key topics of interest include dating the origin and early evolution of lizards, the phylogenetic origin of snakes, the evolution of venom, recent agreements between morphological and molecular squamate evolutionary trees, genomic patterns of evolution, and the integration of morphological and molecular data sets.”

The Simoes and Pyron study also suffers from taxon exclusion by omitting protosquamates.

“We conclude by providing perspectives on possible advancements in the field, directing researchers to promising future lines of investigation that are necessary to further expand our synthetic knowledge of squamate evolution.”

Definition: Synthetic knowledge = “Synthetic statements are based on our sensory data and experience. The truth-value of a synthetic statements cannot be figured out based solely on logic.”

The authors do not suggest ‘adding taxa’ to minimize taxon exclusion and thereby form a more complete understanding of the inclusion set of squamates and their outgroups.

From the text:
“The broader the taxonomic sampling, or the deeper in time we need to go to find the last common ancestor of all sampled species, the greater the likelihood of encountering entirely extinct lineages.”

This is true. Suggestions for taxon inclusion are shown above (Fig. 1).

From the text:
“An accurate understanding of the squamate Tree of Life is thus a crucial basis for reconstructing the evolutionary history of a considerable component of the world’s biodiversity. A robust phylogenetic tree is therefore the necessary starting point towards a broader understanding of the evolvability of functional traits, distribution of extinction risk, origin of life history strategies, and myriad other macroevolutionary dynamics.”

This is true.

From the text:
“Morphological data sets differ strongly in the placement of key fossil groups such as Mosasauria and Paramacellodidae (see Pyron, 2017) and relationships among the major extant families many morphological and molecular data sets appear fundamentally irreconcilable
with respect to the placement of taxa such as Iguania (Losos et al., 2012).

This is true. That is why we must avoid, ignore, omit molecular data.

The authors wrote,
“First, what is the best phylogenetic hypothesis for Squamata, including both extinct and extant lineages?”

The LRT. Following this the authors asked several more specific questions concerning the genesis of various clades and traits.

The authors wrote,
“Here, we review the recent history and future directions of research into the squamate Tree of Life.”

Unfortunately the authors do not immediately ignore all genomic data, but prefer and embrace that data. Don’t get near genomic tests in deep time studies. All extinct taxa are immediately excluded in genomic studies. After that there is no need to expand on the multitude of faults generated by current genomic studies…other than to use them within a well-established genus only. That way we can more probably avoid deep time studies.

The authors list several protosquamates, then note,
they are poorly supported rogue taxa. Rogue taxa need to be included. Expand that taxon list, as in the LRT, and those phylogenetic problems will disappear. Don’t give up! Don’t exclude. Add taxa.

Apparently without testing, the authors accepted the invalid view
that Megachirella was “the oldest known squamate”. In the LRT Megachirella nests as a basal rhynchocephalian, not a squamate. Add taxa to figure this out for yourself.

The authors also make the traditional mistake of assuming
that all diapsid-grade reptiles form a single clade. Testing shows unrelated diapsid-grade taxa arise twce. Again, add tax to find this out for yourself.

Simoes and Pyron report,
“The growing current consensus is that the early part of the lepidosauromorph Tree of
Life consisted of only a few stem taxa before the divergence between rhynchocephalians
and squamates.”

Consensus is politics, not science. There is only correct and incorrect. Add taxa to find out which is which.

Simoes and Pyron state,
“Most notably, the early divergence of gekkotans in the squamate tree has been recovered by essentially all molecular data sets to date and finds agreement in the latest morphological hypotheses. The placement of snakes as the sister lineage to iguaniansþanguimorphans, irrespective of the placement of mosasaurians.”

The LRT refutes those conclusions. Snakes and gekkos share a last common ancestor apart from other extant lineages of squamates.

The authors conclude,
“It may be impossible to obtain a full agreement between morphological and molecular trees, because they represent fundamentally distinct dimensions of organismal evolution and are differentially affected by selective pressures and by fixed and plastic variation in development and ontogeny.”

Agreed! Don’t even try to find full agreement between DNA and traits in deep time studies. Over the long term DNA is affected by endemic viruses.

The authors finish with:
“The development of more complex models of morphological character evolution is paramount to a more biologically realistic modeling of the phenotype, comparable to the array of molecular
substitution models currently available.”

No. Keep it simple. Use traits. Add taxa. It’s as simple as that.

References
de Querioz K, Cantino PD and Gauthier JA 2020. Pan-Squamata, JA Gauthier and K deQueiroz, new clade name. In Phylonyms, a companion to the PhyloCode by de Queiroz K, Cantino PD and Gauthier JA Taylor and Francis, Boca Raton.
Estes R, de Queiroz R, and Gauthier J 1988. Phylogenetic relationships within Squamata.
Pp. 119–281 in Phylogenetic Relationships of the Lizard Families (Estes R and Pregill G, eds.).
Stanford University Press, Stanford, CA.
Simoes TR and Pyron RA 2021. The Squamate Tree of Life. Bulletin of the Museum of Comparative Zoology 163(2): 47-95. doi: https://doi.org/10.3099/0027-4100-163.2.47
https://bioone.org/journals/bulletin-of-the-museum-of-comparative-zoology/volume-163/issue-2/0027-4100-163.2.47/THE-SQUAMATE-TREE-OF-LIFE/10.3099/0027-4100-163.2.47.full
Simòes T, and 8 co-authors 2018. The origin of squamates revealed by a Middle Triassic lizard from the Italian Alps. Nature 557: 706â709

https://pterosaurheresies.wordpress.com/2018/05/31/megachirella-not-at-the-origin-of-squamates-lacertulus-is-older/