Three recent phylogenetic studies used invalid outgroup taxa

Today we’ll look at three recent academic studies
focused on the phylogeny of bats, whales and armadillos. None included a valid outgroup arrived at by testing in a wider gamut phylogenetic analysis like the large reptile tree (LRT, 2340 taxa).

The LRT has 2340 taxa in order to avoid cherry-picking distantly related or intentionally creating all-zero outgroup taxa. Here outgroup taxa have passed the test.

Ghazali et al 2025 looked at whale phylogeny focusing on whale humeri.
Their cladogram split Mysticeti from Odontoceti, but indicated Aegicetus (Fig 1a) was their last common ancestor and only Maiacetus (Fig 1a) preceded it. By contrast, in the LRT Mysticeti evolved from a long series of hippos and desmostylians (Fig 1b) at the same time that Odontoceti evolved separately from a long series of archaeocetes and pakicetids. Tenrecs are living pakicetids in the LRT. The authors concluded, ‘relaxed negative selection and random drift as the likely main evolutionary patterns for the evolution of the humerus shape.’

Taxon exclusion is the number one problem in paleontology. The LRT fixes that problem.
Whale experts are not interested in adding pertinent taxa listed in the LRT. We all await one brave whale expert willing to do so.

Morales et al 2026 looked at bat phylogeny.
Their cladogram cherry-picked an elephant, a mouse, a human, a shrew, a horse, a cow, a pangolin and a mink for outgroup taxa and nested the big fruit bats at the base of their bat phylogeny study. The boldface taxa above formed a clade in Morales et al that nested closest to bats. Equus, the horse, was at that basal node.

By contrast in the LRT bats arise from Microcebus, the smallest primate (Fig 2). Long-tailed bats are basalmost taxa in the LRT, not fruit bats.

BTW, this study broke a record for having 136 co-authors. Apparently not one raised their hand in opposition to posting elephants and horses as outgroup taxa. Editors and referees were also on board with that untenable hypothesis. I find this strange.

Traits are better.

Casali et al 2026 looked at armadillo phylogeny.
The authors reported, “Here, we integrate the largest morphological dataset for cingulates with molecular and stratigraphic data to infer their phylogeny, divergence times, and diversification dynamics. Results support the monophyly of Cingulata and recover two main clades, Paracingulata and Eucingulata. Eucingulata includes Dasypodoidea and Chlamyphoroidea, the latter comprising Euphracta and Glyptodonta.”

Unfortunately this study included the distantly related opossum Didelphis as the basalmost cherry-picked outgroup taxon. Other cherry-picked outgroup taxa included distantly related Cretaceous Ukhaatherium and Asioryctes. This tells the reader the authors had no idea where armadillos and kin came from.

The authors did not realize that unarmored sloths and anteaters are ingroup taxa. Instead they included one of each (Hapalops and Tamandua, Fig 3) as outgroup taxa. The armored pangolin (Manis) was excluded.

To remedy this situation, in the LRT Anagale is the proximal outgroup taxon to the Cingulata (now revised to include sloths, anteaters and pangolins). The tiny, likely subterranean, unarmored armadillo in the LRT, Epoicotherium (Fig 3), is not mentioned.

Wikipedia reports,
“Anagale is an extinct genus of mammal from the Early Oligocene of Mongolia. Its closest living relatives are the rodents and lagomorphs.The build of the hind legs of Anagale indicates that it walked, and did not hop. Judging from its shovel-shaped claws, Anagale burrowed for food, such as subterranean beetles and worms. Anagale fossils have strongly worn teeth from eating soil, further indicating it ate subterranean invertebrates.”

Sounds like a pre-armadillo, doesn’t it? Looks like one, too (Fig 3).

In the LRT
formerly enigmatic Anoplotherium, ancestral to the South American deer-like Litopterna in the LRT, is also ancestral to Mongolian Anagale (Fig 3), which is ancestral to the South American Cingulata in the LRT.

Coincidence? Or was a South America a geographic refugium? Perhaps some of these taxa (like Anagale and Anoplotherium) saw dinosaurs prior to the splitting of the continents.

References
Casali D et al 7 co-authors) 2026. Unravelling the phylogeny of armadillos and their kin (Mammalia, Xenarthra, Cingulata) combining morphological, molecular, and stratigraphic data July 2026Cladistics DOI: 10.1111/cla.70048
Ghazali M et al (8 co-authors) 2025. Humerus shape evolved in cetaceans under relaxed selection and random drift March 2025Communications Biology 8(1) DOI: 10.1038/s42003-025-07952-w
Morales A et al (136 authors) 2026. Reference genomes and fossils revise bat family phylogeny and biogeography September 2026Nature DOI: 10.1038/s41586-026-11007-3

wiki/Cingulata
wiki/Bat
wiki/Whale

Source: https://pterosaurheresies.wordpress.com/2026/09/28/three-recent-phylogenetic-studies-used-invalid-outgroup-taxa/