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North Vietnam is situated on a major route of Pleistocene hominin dispersal in East Asia, and the area's karstic caves preserve many prehistoric shell middens. Fossil and genomic evidence suggest a complex human history in this region and more widely across Southeast Asia and southern China, but related archaeological investigations are hampered by challenging site stratigraphies. Recent investigations of shell middens in other geographical settings have revealed the microstratigraphic complexity of these anthropogenic deposits. But caves promote distinctive site formation processes, while tropical climates may catalyse geomorphic and diagenetic changes. These environmental factors complicate the interpretation of North Vietnam's shell middens and constraining their effects upon the formation, preservation and destruction of these sites is critical to understanding the archaeology of this region. We examine two archaeological cave sites, dated to the Late Pleistocene and located in the limestone uplands surrounding the Hanoi Basin. Each contains multiple shell midden layers associated with prehistoric occupation and burials. Using thin-section micromorphology (microstratigraphy), we reconstruct the depositional and post-depositional histories of these sites, presenting a geoarchaeological framework of interpretation that is applicable to shell middens in mainland Southeast Asia and tropical zones more widely. This work represents a further step towards improving our understanding of prehistoric human dispersals and adaptations in this region.This article is part of the theme issue ���The role of tropical rainforests in the deep human past���.

Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian and American wolves and domestic dogs.1 Genetic studies have suggested these groups trace their origins to a wolf population that expanded during the last glacial maximum (LGM)1, 2, 3 and replaced local wolf populations.4 Moreover, ancient genomes from the Yana basin and the Taimyr peninsula provided evidence of at least one extinct wolf lineage that dwelled in Siberia during the Pleistocene.35 Previous studies have suggested that Pleistocene Siberian canids can be classified into two groups based on cranial morphology. Wolves in the first group are most similar to present-day populations, although those in the second group possess intermediate features between dogs and wolves.67 However, whether this morphological classification represents distinct genetic groups remains unknown. To investigate this question and the relationships between Pleistocene canids, present-day wolves, and dogs, we resequenced the genomes of four Pleistocene canids from Northeast Siberia dated between >50 and 14 ka old, including samples from the two morphological categories. We found these specimens cluster with the two previously sequenced Pleistocene wolves, which are genetically more similar to Eurasian wolves. Our results show that, though the four specimens represent extinct wolf lineages, they do not form a monophyletic group. Instead, each Pleistocene Siberian canid branched off the lineage that gave rise to present-day wolves and dogs. Finally, our results suggest the two previously described morphological groups could represent independent lineages similarly related to present-day wolves and dogs.