A new genomic study of the Carnivora

Beware colleagues.
We learned long ago that genomic studies produce false positives in deep time studies. Genomic studies recover clades named for continents like Afrotheria and Laurasiatheria. So why are workers still dabbling in the dark art of deep time genomics?

From the Hassanin et al. 2020 abstract:
“The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversifications are still a matter of debate.”

Not true. The large reptile tree (LRT, 1747+ taxa) confidently nests Carnivora at the base of the Placentalia with outgroups extending to headless Cambrian chordates. The proximal outgroups and sisters to basal Carnivora look quite similar (Fig. 1) inside and out, even allowing for 200 million years of evolution since their radiation.

Figure 1. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

Figure 1. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

Continuing from the Hassanin et al. 2020 abstract:
“Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora.”

Hold on to your hats. Here comes a load of genomic misdirection.

“According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloidea/Pinnipedia) diverged from each other during the Eocene,”

Phenomic studies, like the LRT, do not recover this clade.

“while all major groups of Feliformia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial divergences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene.”

 Phenomic studies, like the LRT, do not recover this clade. In the LRT, dogs and cats are highly derived sister taxa, along with hyenas and aardwolves. Seals and sea lions arise from separate terrestrial ancestors. Not all bears are related to Ursus. Weasels are basal to all of the above, including a long list of fossil taxa ignored by genomics. Potos flavus is the extant kinkajou, which was just added to the LRT, nesting between Procyon and the pandas, as expected.

Figure 2. Subset of the LRT focusing on the Carnivora.

Figure 2. Subset of the LRT focusing on the Carnivora. Genetta was just added to the LRT, nesting with Paleocenee Protictis.

In the LRT
Vulpavus, Protictis + Genetta and Nandinia are basalmost Placentalia, and the only tested placental outgroups to the Carnivora. Talpa, the mole, is an overlooked extant member of the Carnivora. Ursus arises apart from dogs + cats, which find last common ancestors in Tremarctos, Speothos and Borophagus. The short-faced bear, Arctodus, is a giant wolverine (Gulo). Seals and sea lions have separate terrestrial ancestors and became aquatic by convergence. The rest of the online LRT is here: reptileevolution.com/reptile-tree.htm


References
Hassanin A, et al. (7 co-authors) 2020. Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes. bioRxiv 2020.10.05.326090 (preprint)
doi: https://doi.org/10.1101/2020.10.05.326090
https://www.biorxiv.org/content/10.1101/2020.10.05.326090v1

Genomic studies:
Flynn JJ, et al. 2005. Molecular phylogeny of the Carnivora (Mammalia): assessing the impact of increased sampling on resolving enigmatic relationships. Syst Biol 54:317–37.

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