Multidisciplinary investigations at the Los Ajos archaeological mound complex in the wetlands of southeastern Uruguay challenge the traditional view that the La Plata basin was inhabited by simple groups of hunters and gatherers for much of the pre-Hispanic era. Here we report new archaeological, palaeoecological and botanical data indicating that during an increasingly drier mid-Holocene, at around 4,190 radiocarbon (14C) years before present (bp), Los Ajos became a permanent circular plaza village, and its inhabitants adopted the earliest cultivars known in southern South America. The architectural plan of Los Ajos during the following Ceramic Mound Period (around 3,000-500 14C yr bp) is similar to, but earlier than, settlement patterns demonstrated in Amazonia, revealing a new and independent architectural tradition for South America.

The discovery of an exceptionally well-preserved skull permits the description of the new South American fossil species of the rodent, Josephoartigasia monesi sp. nov. (family: Dinomyidae; Rodentia: Hystricognathi: Caviomorpha). This species with estimated body mass of nearly 1000 kg is the largest yet recorded. The skull sheds new light on the anatomy of the extinct giant rodents of the Dinomyidae, which are known mostly from isolated teeth and incomplete mandible remains. The fossil derives from San José Formation, Uruguay, usually assigned to the Pliocene–Pleistocene (4–2 Myr ago), and the proposed palaeoenvironment where this rodent lived was characterized as an estuarine or deltaic system with forest communities.

The unusual mix of morphological traits displayed by extinct South American native ungulates (SANUs) confounded both Charles Darwin, who first discovered them, and Richard Owen, who tried to resolve their relationships. Here we report an almost complete mitochondrial genome for the litoptern Macrauchenia. Our dated phylogenetic tree places Macrauchenia as sister to Perissodactyla, but close to the radiation of major lineages within Laurasiatheria. This position is consistent with a divergence estimate of ∼66 Ma (95% credibility interval, 56.64–77.83 Ma) obtained for the split between Macrauchenia and other Panperissodactyla. Combined with their morphological distinctiveness, this evidence supports the positioning of Litopterna (possibly in company with other SANU groups) as a separate order within Laurasiatheria. We also show that, when using strict criteria, extinct taxa marked by deep divergence times and a lack of close living relatives may still be amenable to palaeogenomic analysis through iterative mapping against more distant relatives.

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