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Eastern Africa has been a prime target for scientific drilling because it is rich in key paleoanthropological sites as well as in paleolakes, containing valuable paleoclimatic information on evolutionary time scales. The Hominin Sites and Paleolakes Drilling Project (HSPDP) explores these paleolakes with the aim of reconstructing environmental conditions around critical episodes of hominin evolution. Identification of biological taxa based on their sedimentary ancient DNA (sedaDNA) traces can contribute to understand past ecological and climatological conditions of the living environment of our ancestors. However, sedaDNA recovery from tropical environments is challenging because high temperatures, UV irradiation, and desiccation result in highly degraded DNA. Consequently, most of the DNA fragments in tropical sediments are too short for PCR amplification. We analyzed sedaDNA in the upper 70 m of the composite sediment core of the HSPDP drill site at Chew Bahir for eukaryotic remnants. We first tested shotgun high throughput sequencing which leads to metagenomes dominated by bacterial DNA of the deep biosphere, while only a small fraction was derived from eukaryotic, and thus probably ancient, DNA. Subsequently, we performed cross-species hybridization capture of sedaDNA to enrich ancient DNA (aDNA) from eukaryotic remnants for paleoenvironmental analysis, using established barcoding genes (cox1 and rbcL for animals and plants, respectively) from 199 species that may have had relatives in the past biosphere at Chew Bahir. Metagenomes yielded after hybridization capture are richer in reads with similarity to cox1 and rbcL in comparison to metagenomes without prior hybridization capture. Taxonomic assignments of the reads from these hybridization capture metagenomes also yielded larger fractions of the eukaryotic domain. For reads assigned to cox1, inferred wet periods were associated with high inferred relative abundances of putative limnic organisms (gastropods, green algae), while inferred dry periods showed increased relative abundances for insects. These findings indicate that cross-species hybridization capture can be an effective approach to enhance the information content of sedaDNA in order to explore biosphere changes associated with past environmental conditions, enabling such analyses even under tropical conditions.

Our understanding of the impact of climate-driven environmental change on prehistoric human populations is hampered by the scarcity of continuous paleoenvironmental records in the vicinity of archaeological sites. Here we compare a continuous paleoclimatic record of the last 20 ka before present from the Chew Bahir basin, southwest Ethiopia, with the available archaeological record of human presence in the region. The correlation of this record with orbitally-driven insolation variations suggests a complex nonlinear response of the environment to climate forcing, reflected in several long-term and short-term transitions between wet and dry conditions, resulting in abrupt changes between favorable and unfavorable living conditions for humans. Correlating the archaeological record in the surrounding region of the Chew Bahir basin, presumably including montane and lake-marginal refugia for human populations, with our climate record suggests a complex interplay between humans and their environment during the last 20 ka. The result may contribute to our understanding of how a dynamic environment may have impacted the adaptation and dispersal of early humans in eastern Africa. [ABSTRACT FROM AUTHOR]