Carnivora genomic testing: Hassanin et al. 2021

From the abstract:
“The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversification of members of the order are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora.”

Genomic tests too often do not and can not test fossil taxa leading to a problem with taxon exclusion. Moreover, genomic testing in deep time too often delivers false positives relative to phenomic (trait-based) traits that are designed to produce tree topologies in which all sister taxa greatly resemble one another, modeling micro-evolutionary events. Why this is so remains an unsolved problem. A phenomic cladogram (the LRT, subset Fig. x) that includes fossil taxa is found online here: http://reptileevolution.com/reptile-tree.htm

Figure 2. Talpa the Eastern mole nests in the LRT with Herpestes the mongoose.

Figure 1. Talpa the Eastern mole nests in the LRT with Herpestes the mongoose.

Talpa, the mole (Fig. 1), was excluded here, but nests within Carnivora in the phenomic analysis, the large reptile tree (LRT, 1803+ taxa, subset Fig. x).

Figure 1. Nandinia, the palm civet, nests as the proximal outgroup taxon to the Carnivora and all other placental mammals.

Figure 2 Nandinia, the palm civet, nests as the proximal outgroup taxon to the Carnivora and all other placental mammals.

Nandinia, the palm civet sure looks like it, but is not a basal member of Carnivora in the LRT, but a basal placental outgroup taxon to the clade Carnivora.

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 3. 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.

Carnivora is the first major clade to split off
from basal Placentalia (Fig. x). Therefore, the proximal outgroup taxon, the woolly oppossum, Caluromys (Fig. 3) , should be included as the outgroup next time.

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

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

By chilling contrast,
in the Hassanin et al. 2021 genomic analysis, a hoofed placental, the tapir (Tapirus), was used as the outgroup taxon. Given all other placentals for their choice of outgroup for Carnivora, why did they choose a relative of horses and rhinos? We’ve seen this sort of confused mayhem before and recently in genomic studies. Let’s all pray that the ghost of Alfred Sherwood Romer will come visit Hassanin et al. and all others who think this is a good idea.


References
Hassanin A, Veron G, Ropiquet A, Jansen van Vuuren B, Le´cu A, Goodman SM, et al. 2021. Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes. PLoS ONE 16(2): e0240770. https://doi.
org/10.1371/journal.pone.0240770

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