Genomic basis for skin phenotype and cold adaptation in the extinct Steller’s sea cow

Steller’s sea cow, an extinct sirenian and one of the largest Quaternary mammals, was described by Georg Steller in 1741 and eradicated by humans within 27 years. Here, we complement Steller’s descriptions with paleogenomic data from 12 individuals. We identified convergent evolution between Steller’s sea cow and cetaceans but not extant sirenians, suggesting a role of several genes in adaptation to cold aquatic (or marine) environments. Among these are inactivations of lipoxygenase genes, which in humans and mouse models cause ichthyosis, a skin disease characterized by a thick, hyperkeratotic epidermis that recapitulates Steller’s sea cows’ reportedly bark-like skin. We also found that Steller’s sea cows’ abundance was continuously declining for tens of thousands of years before their description, implying that environmental changes also contributed to their extinction

Notiomastodon Supplemental Data

The extinct Gomphotheriidae is the only proboscidean family that colonizedSouth America. The phylogenetic position of the endemic taxa has been throughseveral revisions using morphological comparisons. Morphological studies areenhanced by paleogenetic analyses, a powerful tool to resolve phylogenetic rela-tionships; however, ancient DNA (aDNA) preservation decreases in warmer re-gions. Despite the poor preservation conditions for aDNA in humid, sub-tropicalclimates, we recovered ~3,000 bp of mtDNA of Notiomastodon platensis fromthe Arroyo del Vizcaı́no site, Uruguay. Our calibrated phylogeny places Notio-mastodon as a sister taxon to Elephantidae, with a divergence time of ~13.5Ma. Additionally, a total evidence analysis combining morphological and paleoge-netic data shows that the three most diverse clades within Proboscidea divergedduring the early Miocene, coinciding with the formation of a land passage be-tween Africa and Eurasia. Our results are a further step toward aDNA analyseson Pleistocene samples from subtropical regions and provide a framework forproboscidean evolution.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

Estimating the dwarfing rate of an extinct Sicilian elephant

Evolution on islands, together with the often extreme phenotypic changes associated with it, has attracted much interest from evolutionary biologists. However, measuring the rate of change of phenotypic traits of extinct animals can be challenging, in part due to the incompleteness of the fossil record. Here, we use combined molecular and fossil evidence to define the minimum and maximum rate of dwarfing in an extinct Mediterranean dwarf elephant from Puntali Cave (Sicily).1 Despite the challenges associated with recovering ancient DNA from warm climates,2 we successfully retrieved a mitogenome from a sample with an estimated age between 175,500 and 50,000 years. Our results suggest that this specific Sicilian elephant lineage evolved from one of the largest terrestrial mammals that ever lived3 to an island species weighing less than 20% of its original mass with an estimated mass reduction between 0.74 - 200.95 kg and height reduction between 0.15 - 41.49 mm per generation, respectively. We show that combining ancient DNA with palaeontological and geochronological evidence can constrain the timing of phenotypic changes with greater accuracy than could be achieved using any source of evidence in isolation