Extended longevity of DNA preservation in Levantine Paleolithic sediments, Sefunim Cave, Israel

The fauna from Mughr el-Hamamah, Jordan: Insights on human hunting behavior during the Early Upper Paleolithic

As a corridor for population movement out of Africa, the southern Levant is a natural laboratory for research exploring the dynamics of the Middle-to-Upper Paleolithic transition. Yet, the number of well-preserved sites dating to the initial millennia of the Early Upper Paleolithic (EUP; ∼45-30 ka) remains limited, restricting the resolution at which we can study the biocultural and techno-typological changes evidenced across the transition. With EUP deposits dating to 45-39 ka cal BP, Mughr el-Hamamah, Jordan, offers a key opportunity to expand our understanding of EUP lifeways in the southern Levant. Mughr el-Hamamah is particularly noteworthy for its large faunal assemblage, representing the first such assemblage from the Jordan Valley. In this paper, we present results from taxonomic and taphonomic analyses of the EUP fauna from Mughr el-Hamamah. Given broader debates about shifts in human subsistence across the Middle-to-Upper Paleolithic transition, we also assess evidence for subsistence intensification, focusing especially on the exploitation of gazelle and the use of small game. Taphonomic data suggest that the fauna was primarily accumulated by human activity. Ungulates dominate the assemblage; gazelle (Gazella sp.) is the most common taxa, followed by fallow deer (Dama mesopotamica) and goat (Capra sp.). Among the gazelle, juveniles account for roughly one-third of the sample. While the focus on gazelle and the frequency of juveniles are consistent with broader regional trends, evidence for the regular exploitation of marrow from gazelle phalanges suggests that the EUP occupants of Mughr el-Hamamah processed gazelle carcasses quite intensively. Yet, the overall degree of dietary intensification appears low-small game is rare and evidence for human capture of this game is more equivocal. As a whole, our results support a growing body of data showing gradual shifts in animal exploitation strategies across the Middle-to-Upper Paleolithic transition in the southern Levant.

Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA

Ancient DNA is highly degraded, resulting in very short sequences. Reads generated with modern high-throughput sequencing machines are generally longer than ancient DNA molecules, therefore the reads often contain some portion of the sequencing adaptors. It is crucial to remove those adaptors, as they can interfere with downstream analysis. Furthermore, overlapping portions when DNA has been read forward and backward (paired-end) can be merged to correct sequencing errors and improve read quality. Several tools have been developed for adapter trimming and read merging, however, no one has attempted to evaluate their accuracy and evaluate their potential impact on downstream analyses. Through the simulation of sequencing data, seven commonly used tools were analyzed in their ability to reconstruct ancient DNA sequences through read merging. The analyzed tools exhibit notable differences in their abilities to correct sequence errors and identify the correct read overlap, but the most substantial difference is observed in their ability to calculate quality scores for merged bases. Selecting the most appropriate tool for a given project depends on several factors, although some tools such as fastp have some shortcomings, whereas others like leeHom outperform the other tools in most aspects. While the choice of tool did not result in a measurable difference when analyzing population genetics using principal component analysis, it is important to note that downstream analyses that are sensitive to wrongly merged reads or that rely on quality scores can be significantly impacted by the choice of tool.

Why the geosciences are becoming increasingly vital to the interpretation of the human evolutionary record

Advanced geoscience techniques are essential to contextualize fossils, artefacts and other archaeologically important material accurately and effectively. Their appropriate use will increase confidence in new interpretations of the fossil and archaeological record, providing important information about the life and depositional history of these materials and so should form an integral component of all human evolutionary studies. Many of the most remarkable recent finds that have transformed the field of human evolution are small and scarce, ranging in size from teeth to strands of DNA, recovered from complex sedimentary environments. Nevertheless, if properly analysed, they hold immense potential to rewrite what we know about the evolution of our species and our closest hominin ancestors.

100 years of anthropogenic impact causes changes in freshwater functional biodiversity

Despite efforts from scientists and regulators, biodiversity is declining at an alarming rate. Unless we find transformative solutions to preserve biodiversity, future generations may not be able to enjoy nature's services. We have developed a conceptual framework that establishes the links between biodiversity dynamics and abiotic change through time and space using artificial intelligence. Here, we apply this framework to a freshwater ecosystem with a known history of human impact and study 100 years of community-level biodiversity, climate change and chemical pollution trends. We apply explainable network models with multimodal learning to community-level functional biodiversity measured with multilocus metabarcoding, to establish correlations with biocides and climate change records. We observed that the freshwater community assemblage and functionality changed over time without returning to its original state, even if the lake partially recovered in recent times. Insecticides and fungicides, combined with extreme temperature events and precipitation, explained up to 90% of the functional biodiversity changes. The community-level biodiversity approach used here reliably explained freshwater ecosystem shifts. These shifts were not observed when using traditional quality indices (e.g. Trophic Diatom Index). Our study advocates the use of high-throughput systemic approaches on long-term trends over species-focused ecological surveys to identify the environmental factors that cause loss of biodiversity and disrupt ecosystem functions.