Squamate genes show ‘no support’ for key traditional morphological relationships

If squamate genes showed ‘no support’
for key traditional morphological relationships, that was a red flag that Burbrink et al. 2019 chose to ignore. Instead they put their faith in genes instead of the measurable evidence of traits. As we’ve seen many times before, something is wrong with deep time genetic testing, hobbled from the starting blocks by not including fossil taxa. No gene test has ever revealed that a jugal is absent or present, that a metatarsal is longer than the toe or shorter. Whenever those things happen, we’ll review genomic tests again.

Burbrink et al. 2019 report with great confidence,
“Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups.

The opposite is true, as we’ve seen before.
Genomics is providing false positive family trees that do not match phenomic trees (Fig. 1)… not all the time, but often enough not to trust deep time genomics.

Figure 1.  Subset of the LRT focusing on lepidosaurs and snakes are among the squamates.

Figure 1.  Subset of the LRT focusing on lepidosaurs and snakes are among the squamates. This cladogram includes fossil taxa and documents a gradual accumulation of traits across all taxa. 

Burbrink et al. 2019 report with great confidence,
“Here, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome scale data.

Genomic studies cannot and do not include fossil taxa,
which also puts genomic studies at a great disadvantage. How do you test genomic studies? You test genomic studies with phenomic studies, not the other way around.

Burbrink et al. 2019 report with great confidence,
“We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata.

According to Wikipedia and Variety of Life:
Toxicofera =  proposed clade Serpentes (snakes), Anguimorpha (monitor lizards, gila monster, and alligator lizards) and Iguania (iguanas, agamas, and chameleons). None of this is supported by the LRT.

Scleroglossa = includes anguimorphs, geckos, autarchoglossans (scincomorphs and varanoids), and amphisbaenians. For the most part this is supported by the LRT, but snakes are not listed here and they are related to geckos. Amphisabaenians are scincomorphs.

Macrostomata = non-fossorial snakes. In the LRT (subset Fig. 1) fossorial (= burrowing snakes) are a clade within the non-fossorial snakes. In other words, Burbrink’s team got it backwards, perhaps because no fossil snakes and pre-snakes were included.

“We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; and between the three toxiferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).”

Don’t trust the results recovered by Burbrink et al. 2019. 
Genomic tests in lizards are not supported by validated phenomic tests. Only the LRT (at present) documents a gradual accumulation of traits across extinct and extant lepidosaur and squamate taxa that goes back to jawless Silurian fish.

Sorry guys, no matter how much effort went into creating Burbrink et al. and its supplementary data with 15 co-authors, it turned out not to provide any insights into squamate evolutionary events and therefore, was a waste of time. Worse yet, it promoted false positives as good science.

Next time,
before promoting genomics above phenomics, test genomics against phenomics.  Yesterday we looked at a possible reason why genomic tests do not replicate phenomic tests.


References
Burbrink FT et al. (14 co-authors) 2019. Interrogating genomic-scale data for Squamata (lizards, snakes, and amphisbaenians) shows no support for key traditional morphological relationships. Systematic Biology, syz062 (advance online publication)
doi: https://doi.org/10.1093/sysbio/syz062
https://academic.oup.com/sysbio/advance-article-abstract/doi/10.1093/sysbio/syz062/5573126

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