Evolution of the ancestral mammalian karyotype and syntenic regions.

Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for ∼320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes.

Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates.

The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19. The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of ACE2 sequences from 410 vertebrate species, including 252 mammals, to study the conservation of ACE2 and its potential to be used as a receptor by SARS-CoV-2. We designed a five-category binding score based on the conservation properties of 25 amino acids important for the binding between ACE2 and the SARS-CoV-2 spike protein. Only mammals fell into the medium to very high categories and only catarrhine primates into the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 spike protein binding and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (frequency <0.001) variants in 10/25 binding sites. In addition, we found significant signals of selection and accelerated evolution in the ACE2 coding sequence across all mammals, and specific to the bat lineage. Our results, if confirmed by additional experimental data, may lead to the identification of intermediate host species for SARS-CoV-2, guide the selection of animal models of COVID-19, and assist the conservation of animals both in native habitats and in human care.

Biology and Cultural Importance of the Narwhal.

Though narwhal have survived multiple ice ages, including 2.5 Ma and the last interglacial period with warming temperatures, Arctic climate change during the Anthropocene introduces new challenges. Despite their evolutionary connection to Arctic Pleistocene fossils, narwhal archeocete ancestors from the Pliocene (Bohaskaia monodontoides) and Miocene (Denebola and Odobenocetopsidae) inhabited warm waters. Narwhal Arctic adaptation holds valuable insights into unique traits, including thin skin; extreme diving capacity; and a unique straight, spiraled, and sensory tooth organ system. Inaccessible weather, ice conditions, and darkness limit scientific studies, though Inuit knowledge adds valuable observations of narwhal ecology, biology, and behavior. Existing and future studies in myriad fields of physical, chemical, biological, and genetic science, combined and integrated with remote sensing and imaging technologies, will help elucidate narwhal evolution, biology, and adaptation. When integrated with Qaujimajatuqangit, "the Inuit way of knowing," these studies help describe interesting biologic expressions of the narwhal.

Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates.

The novel coronavirus SARS-CoV-2 is the cause of Coronavirus Disease-2019 (COVID-19). The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of 410 vertebrates, including 252 mammals, to study cross-species conservation of ACE2 and its likelihood to function as a SARS-CoV-2 receptor. We designed a five-category ranking score based on the conservation properties of 25 amino acids important for the binding between receptor and virus, classifying all species from very high to very low. Only mammals fell into the medium to very high categories, and only catarrhine primates in the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 binding, and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (<0.1%) variants in 10/25 binding sites. In addition, we observed evidence of positive selection in ACE2 in multiple species, including bats. Utilized appropriately, our results may lead to the identification of intermediate host species for SARS-CoV-2, justify the selection of animal models of COVID-19, and assist the conservation of animals both in native habitats and in human care.

Sensory ability in the narwhal tooth organ system.

The erupted tusk of the narwhal exhibits sensory ability. The hypothesized sensory pathway begins with ocean water entering through cementum channels to a network of patent dentinal tubules extending from the dentinocementum junction to the inner pulpal wall. Circumpulpal sensory structures then signal pulpal nerves terminating near the base of the tusk. The maxillary division of the fifth cranial nerve then transmits this sensory information to the brain. This sensory pathway was first described in published results of patent dentinal tubules, and evidence from dissection of tusk nerve connection via the maxillary division of the fifth cranial nerve to the brain. New evidence presented here indicates that the patent dentinal tubules communicate with open channels through a porous cementum from the ocean environment. The ability of pulpal tissue to react to external stimuli is supported by immunohistochemical detection of neuronal markers in the pulp and gene expression of pulpal sensory nerve tissue. Final confirmation of sensory ability is demonstrated by significant changes in heart rate when alternating solutions of high-salt and fresh water are exposed to the external tusk surface. Additional supporting information for function includes new observations of dentinal tubule networks evident in unerupted tusks, female erupted tusks, and vestigial teeth. New findings of sexual foraging divergence documented by stable isotope and fatty acid results add to the discussion of the functional significance of the narwhal tusk. The combined evidence suggests multiple tusk functions may have driven the tooth organ system's evolutionary development and persistence.

Vestigial tooth anatomy and tusk nomenclature for monodon monoceros.

Narwhal tusks, although well described and characterized within publications, are clouded by contradictory references, which refer to them as both incisors and canines. Vestigial teeth are briefly mentioned in the scientific literature with limited descriptions and no image renderings. This study first examines narwhal maxillary osteoanatomy to determine whether the erupted tusks are best described as incisiform or caniniform teeth. The study also offers evidence to support the evolutionary obsolescence of the vestigial teeth through anatomic, morphologic, and histologic descriptions. Examination of 131 skull samples, including 110 museum skull specimens and 21 harvested skulls, revealed the erupted tusks surrounded by maxillary bone over the entire length of their bone socket insertion, and are thus more accurately termed caniniform or canine teeth. The anatomy, morphology, and development of vestigial teeth in five skull samples are more fully described and documented. Vestigial tooth samples included 14 embedded pairs or individual teeth that were partially exposed or removed from the maxillary bone. Their location was posterior, ventral, and lateral to the tusks, although male vestigial teeth often exfoliate in the mouth lodging between the palatal tissue and underlying maxillary bone. Their myriad morphologies, sizes, and eruption patterns suggest that these teeth are no longer guided by function but rather by random germ cell differentiation and may eventually cease expression entirely. The conclusions reached are that the narwhal tusks are the expression of canine teeth and that vestigial teeth have no apparent functional characteristics and are following a pattern consistent with evolutionary obsolescence.