Klein et al. 2021 “combined an extensive molecular dataset with phylogenetically and stratigraphically constrained fossil calibrations to infer an evolutionary timescale for Serpentes.”
Once again: molecules. Beware of molecules. They deliver false positives in deep time studies due to endemic, geographic viruses that invade the ‘molecules’. You don’t have to trust traits. You can see them, measure them, watch them evolve. Molecules make you recover foolish cladograms and send them off to the editors of Nature… where they get approved and published!!!
Klein et al. test 115 snake taxa and 54 outgroups (see below).
the large reptile tree (LRT, 1936+ taxa; subset Fig. 1) currently includes very few extant terrestrial snake taxa, it does have a very long list of snake ancestors and a pretty good list of fossorial taxa.
So let’s see how things match up: traits vs. molecules in snakes,
remembering always that snake fossils are extremely rare on this planet.
Klein et al. report,
“Historically, squamates were believed to have experienced minimal extinction at the K-Pg boundary. However, analysis of the K-Pg transition in western North America found evidence for high rates of extinction among squamates, although it remains unclear whether this pattern holds on a global scale.”
“The early fossil record of crown group snakes is fragmentary, often restricted to vertebrae and
afflicted by relatively high rates of homoplasy.” As noted above.
“So far, molecular divergence time analyses of snakes recover conflicting patterns. Most
studies (they cite four) suggest that the majority of extant snake clades diverged in the Cretaceous, although several analyses (they cite three) hint at a more recent diversification of the major subclade Alethinophidia [= all snakes other than blind snakes and thread snakes].”
in the LRT (subset Fig. 1) blind snakes and thread snakes are the most derived fossorial snakes and they arise from members of the Alethinophidia like Loxocemus and Xenopeltis. So Alethinophidia, as defined, is paraphyletic in the LRT. The problem is: in Klein et al. highly derived blind snakes (Figs. 2, 3) are basal to more plesiomorphic terrestrial snakes. This makes the Klein et al. cladogram upside-down phylogenetically.
“Our results suggest a potential diversification of snakes near the time of the K-Pg transition. We find a pattern of increasing vertebral disparity in the aftermath of the extinction, with concurrent increases in average and maximum body size, and dispersal to previously unoccupied landmasses.”
Insert: a bit of backstory.
Tiny four-legged Early Cretaceous Tetrapodophis (16cm; Fig. 1) and and even tinier Barlochersaurus (1.5cm; Fig. 1) are proximal outgroups to all extant snakes in the LRT. So they start small, phylogenetically miniaturized. Snakes split immediately into terrestrial and semi-fossorial forms with Late Cretaceous Dinilysia (88mya, 1.8m in length est) at the base of ‘terrestrial’ snakes.
Older (95mya), smaller (1m) and swimming, Pachyrhachis also nests among the paucity of ‘terrestrial’ snakes in the LRT.
Much smaller Najash (Late Cretaceous, 90mya; 2cm skull) nests at the base of the fossorial snakes in the LRT.
These dates are probably much later than that initial dichotomy and radiation.
Instead these dates more likely represent maximum dispersal. With a sample of one, anything can happen statistically.
The authors used 169 taxa in their analysis.
They chose (= cherry-picked) ten non-squamate amniote and 44 non-snake squamate outgroups, rather than letting the software recover three or four actual proximal outgroups. Included among the 44 were Homo, the human, Gallus, the chicken, Chelydra, the turtle, and Mus the mouse. This is sad. Trait analysis would never have to use these unrelated taxa in a snake analysis.
Technical note on the published cladogram:
In order to read the illegible p39 SuppFig consensus tree of Klein et al. you have to open the page in Photoshop using a 300 dpi setting and still the type is fuzzy from over-magnification. They did not use vector graphics, which enable unlimited magnification.
Distinct from the LRT, highly derived geckos are recovered by Klein et al. at the basal node for squamates. As you’ll note above (Fig. 1) when traits and fossils are employed, geckos are not the most primtive squamates, but are the closest extant snake relatives in the LRT.
Distinct from the LRT, chameleons and anolids are proximal snake outgroups recovered by Klein et al.
Distinct from the LRT, the most derived blind snakes nest as basal snake taxa recovered by Klein et al. And these give rise to less derived, more plesiomorphic fossorial snakes. And these give rise to less derived, more plesiomorphic terrestrial and aquatic snakes.
Distinct from the LRT Klein et al. nest arboreal chameleons with burrowing blind snakes (with no transitional taxa between them).
Because Klein et al. trusted deep time molecules, their cladogram is upside-down.
Apparently no one on their team, or the editors at Nature, or the PhD referees objected to the bizarre results. Folks, this is the paleo-university system in a nutshell. If this is what you want, go for it, pay for it, have your professors tell you what they want you to study. If not, then collect your own trait-based data, run your own analysis, and see for yourself how snakes evolved. Ironically, for budding paleontologists, molecular studies omit the fossils they want to study.
Without a valid, sensible trait-based cladogram that includes fossils
all the work that follows (and there was a lot of work that followed in Klein et al.) is not dubious, or suspect, but a waste of time. Apparently they are teaching university students that molecules deliver better results than traits and fossils. They don’t. Study the bones and study the fossils and learn something.
The cladograms on SuppData pp. 42–44 are also nearly illegible due to the amount of data and the standard page size. Question: why are digital data restricted to page size? It’s illegible when printed. Why not increase the digital page size? The LRT is 25 inches tall and has vector-based PDF files that support it. PDF images can be enlarged to any size without degradation.
Klein CG et al. (5 co-authors) 2021. Evolution and dispersal of snakes across the Cretaceous-Paleogene mass extinction. Nature https://doi.org/10.1038/s41467-021-25136-y Don’t forget to download the SuppData, which has at least 29 figures and 6 tables.