The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the "two-layer" hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.

During the last glacial–interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1–8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe–tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe–tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.

Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago1 had climates resembling those forecasted under future warming2. Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11–19 °C above contemporary values3,4. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare5. Here we report an ancient environmental DNA6 (eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.

Aim Global sea-level rise (SLR) could be as much as 1.8 metres by 2100, which will impact coastal wetland communities and threatened species. We evaluated the likely outcomes of SLR for wetland communities using a process-based simulation model and coupled this with a metapopulation model for a threatened native rodent (Xeromys myoides). Furthermore, we tested the amplified impacts of SLR, urban growth and introduced predators on X. myoides persistence.Location South-east Queensland, Australia.Methods We adapted the Sea Level Affects Marshes Model to subtropical Australia. We used LiDAR elevation data, field data to parameterize surface accretion and shallow subsidence, and local knowledge to configure wetland transitions. SLR was simulated based on the IPCC B1 and A1FI scenarios, as well as the maximal limit of 1.8 m by 2100. Further, we coupled our demographic model to projected shifts in wetland habitat, and estimates of future wetland loss to urban expansion and feral cat (Felis catus) predation.Results Our models project a general decline in wetland communities under SLR, with a noted exception of mangroves. Under the A1FI scenario, SLR allows mangroves to migrate inland, with urban development acting as an obstruction in some areas. Mangrove expansion provides an unexpected benefit for dependent X. myoides populations, although the inclusion of predation and habitat loss due to urban development still suggests extirpation in c. 50 years.Main conclusions Through this case study, we illustrate the usefulness of process-based SLR models in understanding outcomes for wetland communities and dependent species. Our models will underscore decision-making in a dynamic system, with global applications for urban planning, conservation prioritization and wildlife management.

Over the past three decades, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, today the field stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field.

Identifying the causes of similarities and differences in genetic disease prevalence among humans is central to understanding disease etiology. While present-day humans are not strongly differentiated, vast amounts of genomic data now make it possible to study subtle patterns of genetic variation. This allows us to trace our genomic history thousands of years into the past and its implications for the distribution of disease-associated variants today. Genomic analyses have shown that demographic processes shaped the distribution and frequency of disease-associated variants over time. Furthermore, local adaptation to new environmental conditions-including pathogens-has generated strong patterns of differentiation at particular loci. Researchers are also beginning to uncover the genetic architecture of complex diseases, affected by many variants of small effect. The field of population genomics thus holds great potential for providing further insights into the evolution of human disease.

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

The mean state of the tropical Pacific ocean-atmosphere climate, in particular its east-west asymmetry, has profound consequences for regional climates and for the El Niño/ Southern Oscillation variability. Here we present a new high-resolution paleohydrological record using the stable-hydrogen-isotopic composition of terrestrial-lipid biomarkers (δDwax) from a 1,400-year-old lake sedimentary sequence from northern Philippines. Results show a dramatic and abrupt increase in δDwax values around 1630 AD with sustained high values until 1900 AD. We interpret this change as a shift to sustained El Niño-like mean state conditions, and consequently, significantly drier conditions in the western tropical Pacific during the second half of the Little Ice Age. Our findings highlight the prominent role of the tropical Pacific in shaping the hydrology of the Tropics during the Little Ice Age and demonstrate that a marked transition in the tropical Pacific mean state can occur within a human lifetime.